I recently upgraded to:
T-bird 2.0.0.6 Portable.
Enigmail 0.95.3
GnuPG 1.4.7
I am not entirely sure whether this is a T-Bird problem or not, but it started after upgrading to the newest T-Bird Portable.
I have all the above on my USB flash drive.
OpenPGP preferences point to GnuPG in k:\gnupg\gpg.exe
Key manager will not see my keys on k:\ instead it is creating a new keyset in C:\Documents and Settings\Owner\Application Data\gnupg
I did not have this problem with previous releases.
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If you run GPG by itself, it will use %appdata%.
Vintage!
I had to edit the registry entry for the GnuPG keyrings
HKEY_CURRENT_USER\Software\GNU\GnuPG
HomeDir k:\GnuPG (the path to GnuPG on my flash drive)
I can now keep my keys on my USB flash drive and have full GPG functionality.
C:\Documents and Settings\Owner\Application Data\gnupg is now an empty folder.