Here is a snippet of trace, and a screenshot which should answer your question:
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Processing msgs in folder
ProcessUserEx
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Current File Rollover Settings: 100Mb
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10013 19:44:16.046 [3696] (ArchiveTask) <4880> EV:H {CArchivingAgent::ProcessUserEx:#17836} Processing mbx [/o=EV Training/ou=First Administrative Group/cn=Recipients/cn=jeff1], mode [RN_ARCHIVING (0x1)], report mode [False].
10027 19:44:16.109 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::ProcessUserEx:#17888} Calling FindUser() LegacyMbxDn = /o=EV Training/ou=First Administrative Group/cn=Recipients/cn=jeff1 ExchangeFQDN = ev.local ExchSearchPath = GC://exch1.EV.Local
10052 19:44:16.187 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::ProcessUserEx:#18244} Checking Mailbox Site [/o=EV Training/ou=First Administrative Group/cn=Recipients/cn=jeff1]. HR[0x0]
10071 19:44:16.234 [3696] (ArchiveTask) <4880> EV:H {CArchivingAgent::ProcessUserEx:#18662} Mbx [/o=EV Training/ou=First Administrative Group/cn=Recipients/cn=jeff1] is enabled and ready for processing.
10086 19:44:16.265 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::ProcessUserEx:#18726} Mailbox Folder Policy : Using users default policy
10205 19:44:16.359 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [Top of Information Store]
10257 19:44:16.406 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [1Year]
10311 19:44:16.453 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [1Year-testsubs]
10360 19:44:16.515 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [s1]
10413 19:44:16.546 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [Calendar]
10454 19:44:16.593 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [Contacts]
10497 19:44:16.609 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [Drafts]
10551 19:44:16.640 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [Inbox]
10749 19:44:17.579 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [100 items 2]
10831 19:44:17.610 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [1000 items]
11003 19:44:18.048 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [jashd kasdk jahsdkj ahsdkjashd kajshd kajsdh]
11059 19:44:18.079 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [archiveleaverstestfolder]
11156 19:44:18.173 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [EVArchiveSize]
11267 19:44:18.298 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [modified ret cat]
11350 19:44:18.361 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [s2]
11438 19:44:18.501 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [TestFolder1]
11523 19:44:18.658 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [Journal]
11564 19:44:18.673 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [Junk E-mail]
11605 19:44:18.705 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [News Feed]
11646 19:44:18.720 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [Notes]
11687 19:44:18.736 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [Outbox]
11728 19:44:18.751 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [Private1]
11780 19:44:18.798 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [Restored Items]
11819 19:44:18.814 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [ 28/03/2012 13:52:26]
11860 19:44:18.830 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [ 28/03/2012 13:53:37]
11911 19:44:18.877 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [ 28/03/2012 13:54:12]
11954 19:44:18.892 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [RSS Feeds]
12008 19:44:18.939 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [Sent Items]
12050 19:44:18.955 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [Suggested Contacts]
12091 19:44:18.970 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [Sync Issues]
12130 19:44:19.002 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [Conflicts]
12171 19:44:19.017 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [Local Failures]
12212 19:44:19.033 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [Server Failures]
12255 19:44:19.049 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [Tasks]
12296 19:44:19.064 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [TestFolder2]
12347 19:44:19.111 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [x1]
12396 19:44:19.158 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [J123]
12447 19:44:19.221 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [Personal Folders]
12496 19:44:19.252 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [t1]
12549 19:44:19.314 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [Personal Folders 1]
12598 19:44:19.361 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [alpha1]
12651 19:44:19.393 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [Personal Folders 2]
12700 19:44:19.440 [3696] (ArchiveTask) <4880> EV:M {CArchivingAgent::processMessages:#4826} Processing msgs in folder [jongo1]
12732 19:44:19.471 [3696] (ArchiveTask) <4880> EV:H {CArchivingAgent::ProcessUserEx:#19019} It took [3.431399] seconds to process mailbox [/o=EV Training/ou=First Administrative Group/cn=Recipients/cn=jeff1].
And the screenshot:
So, the folders are processed in order... down from the Top of the Information store (ie the mailbox root). The eligible items are added to queues for processing.
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