I know about that limitation and I think Calibre may write a larger title, but there is no way to be sure since there is no way to access the metadata... I get the error I told you about even if I don't try to modify the metadata, only read it. Not to mention I also get that error if I try to modify it. So as far as mobi2mobi is concerned the file is ruined.
You could see if Mobiunpack.py will unpack the problem mobi(s). If it does, you could rebuild them with kindlegen or whatever. That would still leave tracking down where the bogus db name is coming from, of course. Were there any special/unusual characters in the title before you modified it with mobi2mobi/calibre?
Also, have you tried using the command-line version of mobi2mobi to see if the problem might be limited to mobi2mobi-gui?
Can you give one of the titles that seem to trigger the problem (exactly as it was entered)?