Right. Nexus complains about (at least) two missions having the same number, which is more or less a Skirmisher issue. Sorry about that.
There is a experimental fixed version of the Skirmisher with that issue fixed in the thread linked to by DreamorCZ, more specifically in this post:
http://arparso.de/nexus/forum/index.php/topic,91.msg794.html#msg794In order to get the game into working condition again, you'll still need to find the offending missions (or just delete and reinstall Stargate mod), so have a look at Stargate's mod folder in:
universe\mod_missions
Open up each .mission file and look at the top of the file for "MISSION X", where X is a number. If you find two missions with the same number, delete one of these two .mission files or change the number of one of them. Nexus should then be able to start the mod again.
Alternatively, just uninstall the mod (delete the mod's folder) and reinstall. When creating new missions, use the fixed Skirmisher EXE.
(I added the patch to the downloads page now, so you can grab it
there, too)