I have a support call in with Symantec regarding this issue, but I thought I'd check here to see if anyone else had come across this issue.
Before everyone says to check out this article and that article relatings to RIS, I do not have RIS installed! I have gone to many lengths to get this through to Symantec Support and after about four emails with RIS related articles, I think that they now understand my server setup 
My server is Windows Storage Server 2003 64-bit, running BE 12.5 with all the latest patches. Single Instance Storage is installed on the server and it is saving us a handy amount of space, so uninstalling SIS is not going to happen.
I continually get messages like: The item D:\481359a4-d0c5-11dd-8f2e-001a64258d50.sis in use - skipped. In fact I get 41 of these messages, all for different .sis files. The SIS Common Store Folder exists on D:\ drive and is not selected to be backed up.
We were able to get a work around by backing the files up via network shares, however this more than doubles the amount of time it takes to complete the backup job. Obviously having a backup job running for 16 hours instead of 7.5 is not practicle.
If anyone has had this issue and has some tips and/or suggestions as how to resolve it, they would be appreciated.
Don't forget, it is a Windows 2003 server and RIS is not installed.
If/when I get a solution through the support call, I'll post it here if no-one else has posted anything.
Thanks 
