I found out that the repackager doesn't completely capture Thunderbird installation. It is fine with capturing files and registry entries.
But, there are two things it misses out:
1. Registering Thunderbird as email client. When you go to Internet Options ->Program Tab. -> Email and Thunderbird is not listed
as a valid email client
2. Registering Thunderbird MAPI library as COM+ application. When it comes to interact with other applications , ie: sending emails
from Microsoft word should launch Compose window from Thunderbird ( of course , if Thunderbird is configured as default email application)
I gave up using Repackager as the MSI generated by Advanced installer was causing me problems afterwards.
Could you please clarify whether there is another one to create MSI file for Thunderbird, which does address the above issues too?