Current version should not have this issue. It was an old bug around some Windows versions not having the registry key already in existence (although it should exist) and the launcher not interpreting that properly. TBP 3.1.6 should not have this issue and has code specifically to test and correct for this case (see lines 398-402 and 435-436 in ThunderbirdPortable.nsi). TBP 22.214.171.124 is no longer supported so any bugs in it won't be addressed and should not be seen as confirmation of a bug in a current release.
If you are able to get the bug to re-appear with a current release, please post the steps you did to reproduce it and I'll go about trying to reproduce and address the specific condition.
In the meantime, I have updated the bug to detail the issue as it definitely does not occur on any PC where HKCU\Software\Microsoft\Windows\CurrentVersion\UnreadMail already exists and doesn't appear to occur for most users where it doesn't. If there is a regression and it does occur on some versions of Windows, it would leave your account name there (which some users may inadvertently set to their email address).
Last I checked, this bug existed in all unlicensed versions of TB done portably but does not exist in ours. At least it didn't about 2 point releases ago. I'll check to see if there is a regression in that code and if there is, do a revision of both TBP and SMP tomorrow morning (NY time).
When this happened last time (quite a while ago as I recall), I wrote a utility to fix the counts and remove the additional entries in the registry and reset the mail counts:http://johnhaller.com/jh/useful_stuff/r ... il_counts/
(it may give an error about not installing properly on Vista/7 but that error can be ignored)