"So the archives don't show up in the Admin Console list but do show up in the Export wizard."
Yes
"you've exported the data succesfully frpom all of them and you are running EV5 SP3..."
Yes
"...but some of the archives (the problem ones?) are still EV4/unstructured?"
Yes, probably, they are not in the list of archives waiting to be converted, nor do they appear in the list of archives that can be selected to convert. Right now, the only place I see them listed is in the Usage report and in the Export list. They do not appear in any convertarchive list, nor in the enable or disable list, nor in the admin console under mailboxes.
"My first thought is that you might be running a version 4 installation of the VAC (Admin Console) and trying to view structured vaults. Is this possible?"
No I do not believe so. I can see both structured and unstructured archives in the admin console. To be honest, I posted the two problems separately because I did not believe they were related, however, perhaps there is a correlation I'm not seeing. So, just to verify, how would I know what version of the console I'm using?