The latest version of avast home/pro is 4.7.844 31-05-2006 where are you getting the version information from ?
What is your operating system ?
avast can scan multiple pop3 accounts and if you have winXP, win2k, there should be any set-up to do as the Internet Mail provider acts transparently so if your email account details are correct it should work with multiple pop3 accounts.
However, I don't use Thunderbird, so I can't say how the multiple profiles/identities (rather than simply multiple pop3 accounts) might impact on scanning. But I would assume if you are logged in under a profile/identity in tbird that the accounts for that identity would be scanned.
If you could explain the problems you are experiencing, any warnings/errors, etc. it could help especially for those avast members that use tbird.