I am running 3.1 build 121 with 3 MSN accounts, all under 1 identity, & I am NOT having the problem. I went in & looked at buddies.xml & all my MSN contacts have the 3A0 on them, not 3A1. I think you are on to something! I can tell you how to correct your buddy list but not how it ends up with 3A1 in it - for that, you'll have to wait on the devs...
1. Close Trillian
2. Navigate to your profile folder, usually either Program Files\Trillian\Users\(default or profile name) for W9x/ME or any other OS with a new install OR Documents & Settings\(OS User Name)\Trillian\User Settings\(Identity Name) for W2K/XP. If you're not sure, before you close Trillian, choose Trillian, Trillian Preferences, Advanced, Shared Trillian, click your own identity & then Change - look at the folder setting.
3. Make a backup copy of buddies.xml
4. Richt click buddies.xml, Open With... Notepad
5. Choose Edit, Replace on the menu
6. Find 3A1, replace with 3A0, match case
7. Save your changes
8. Fire Trillian back up & you should be fixed
