I am also experiencing this bug in Karmic with updated thunderbird and firefox. 
I discovered that the problem is that I am running firefox with "--no-remote" 
option. It seems that this enables the environment variable MOZ_NO_REMOTE, 
which affects thunderbird also. Running thunderbird with "env -u MOZ_NO_REMOTE" 
solves the bug for me.
Actually, I find quite strange that this env variable is common to both 
programs, since they are completely independent processes and have independent 
profiles.

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mailto link always attempts to open a fresh thunderbird instance
https://bugs.launchpad.net/bugs/12097
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