I upgraded from Thunderbird 3 to 5 via the PortableApps Updater. After updating Thunderbird told me (unexpectedly) that some of my plugins weren't compatible. I performed a check for extension updates, applied the updates, restarted Thunderbird and all was well.
The next day I attached my drive to a different computer and Thunderbird was telling me again that the extensions weren't compatible. I followed the same procedure of updating and everything was fine and posted the issue on the release announcement page.
At JTH's request, I coped my Thunderbird folder (one I had just updated the extensions on) and renamed it to ThunderbirdPortable2 and ran it, and some of the extensions came up as not compatible. Those extensions were :
G-Hub Lite 2.3.0 (https://addons.mozilla.org/en-us/thunderbird/addon/google-hub-google-tab...)
MinimizeToTray revived (MinTrayR) 0.9.4 (https://tn123.org/mintrayr/)
I closed that instance of Thunderbird and re-opened my original one and it again told me the extensions weren't compatible and added a new one to the list :
New Mail Attention 1.2 (https://addons.mozilla.org/en-us/thunderbird/addon/new-mail-attention/)
After all this I had to reboot my computer for an Adobe update (they're getting as bad a MS) and when my computer came back up again Thunderbird said those same 3 plugins weren't compatible, and I had to update them again.