You still didn't answer my questions.
What OS? Win98, XP, Vista, Whatever.
What TB version? 3.95.3 or 3.95.6?
You mentioned an upgrade, what was your previous version?
Now we're at it, try this:
Close TB.
Check in your mail directory whether you've got a tbuser.def or tbuser.eef file, if so rename it to tbuser.def.old (or tbuser.eef.old)
Start TB
BTW I still don't know what you mean with boxes that don't appear at the messages? I've never seen any options boxes at the message list.
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I'm just a user of The Bat! I don't work for Ritlabs.