This problem usually results from using Winzip to extract the mod. It creates an extra mod folder, changing the mod path to (I'll use Kitkun's example) Sins of a Solar Empire\Mods-Entrenchment v1.03 (or Sins of a Solar Empire v1.17)\Dynamic\Dynamic\GameInfo. This extra Mod folder (in this case Dynamic) allows you to enable the mod, but the game only checks the first Dynamic folder, not the second one. Copy everything from the second dynamic folder into the first one, and the mod should work.

If there's no effect, then that's because it can't find the changed files and so applies the standard files as a kind of backup system. Either that, or the mod files aren't actually different.