Emails stored in Data\profile AND "default profile" - borked import

Using Thunderbird Portable (non-beta) on both devices (before and after moving)
XP Pro, SP2
Multiple accounts, each using their own folder hierarchy (NOT in Local Folders by default, but I was sorting them into sub-folders in Local Folders)

So when I went to move my copy of Thunderbird Portable over to another drive, I did a fresh install (I don't know why I did this in retrospect, I should have just copied the whole thing over) I copied over the profile in Data\profile into the new copy of Thunderbird Portable.

(I was moving from an external HD to my Ipod, which is becoming my portable storage device)

However, I was missing much of the email that I had - digging around on the portableapps.com site, I noticed that there was a "default profile" and I also noticed a significant size difference (several hundred megabytes) in the app folders. Figured out that it had been using the default profile to store *some* email, and some went into the Data\profile folder.

This was after I'd used it for a few days, so I don't know what went out of sync, but now if I "read" a message, there is a good chance it will just "disappear" within 24 hours. For now, I'm starting over on a default Thunderbird install, as these are critical (new job) messages that are disappearing

Thankfully I hadn't deleted *most* of them from the server, so I'm okay, for now...

But I want to know why Thunderbird was using both the Default Profile (App\DefaultData) and the base profile (Data\profile) to store messages. Is this a Portable-Apps issue, or is it a Thunderbird issue? (So I know how to proceed with attempting to fix/document it)

Thanks, and feel free to ask any questions to help further identify it. I'm not deleting the moved copy over yet, until I'm sure I've got everything I need.