What version and expansion was the mod made for?
What version of what expansion are you trying to get it to work on?
Sins Mods are very specific to version and expansion type. There are 3 different games in Trinity, each with there own folder for different updates.
- Sins of a Solar Empire --> ...\Mods-vX.XX
- Sins of a Solar Empire Entrenchment --> ...\Mods-Entrenchment vX.XX
- Sins of a Solar Empire Diplomacy --> ...\Mods-Diplomacy vX.XX
vX.XX is the version of the selected expansion. There maybe multiple folders for different versions of each upgrade. Place the mod in the most current version folder only if the mod was made for that version of that expansion. Older version folders or the mods in them are no longer used by the game.
If you have upgraded the game and can no longer use your favourite mod you can try harpo's Mod Updater. This will not always work and you can check and post in the appropriate mod thread for it to be upgraded to the latest version.