Folder Settings saved from Computer to Computer

First the backstory: I have a 2.0Gb thumb drive that I have portableapps running on. I use ThunderbirdPortable to allow me to keep my personal mail in one app when at I'm at work and home. The work machine is a Windows XP SP2 machine, the home machine is a Windows Vista Home Premium machine.

The issue: For the longest time I had no problems, however of late (and I'm kicking myself as a former Systems Administrator for not making exact note of when it started), I get this oddity where the following typical scenario occurs:

I check my mail at work, my rules move items to various folders. I leave a couple of those items unread. I respoond to a couple of items, but because the SMTP ports are blocked, I "Send Later" go about my business, close the program and take it home. (No crashes or anything like that.) At home, I open the program, send the unsent messages, read my unreads, get some new messages that I leave unread, and head back to work the next day. When I open TB at work again, it shows me the unread statuses as they were yesterday when I left (including prompting me to send the now non-existent unread messages). And if I were to take the program home again and plug it in, it keeps the unread statuses as they were before I went to work that day.

I hope that seems to make sense, I can try to explain further. So far as I can tell the only two variables that have changed that have caused this problem in a non-crash situation are: Home PC changed to a Windows Vista PC and TB upgraded to 2.0.0.6. I have since then reinstalled the most recent build of the ThunderbirdPortable.exe just to make sure that wasn't it. Any insights into this? It makes checking my email each time I log in a chore because I can't rely on the read/unread statuses and have to check each folder separately.

Thanks,
Jack