I have read and reread your "problem", and now I am almost certain I know what's causing it.
You must be using Windows Vista, as I don't think this problem occurs with anything else.
Step 1: Go to your mod's folder.
Step 2: Click "Compatibility Files"
Step 3: Copy all the text files you see there.
Step 4: Paste them over the ones in your mod's actual folder.
Done. I expect that's your problem, but hey, I could be wrong...
You must be using Windows Vista, as I don't think this problem occurs with anything else.
Step 1: Go to your mod's folder.
Step 2: Click "Compatibility Files"
Step 3: Copy all the text files you see there.
Step 4: Paste them over the ones in your mod's actual folder.
Done. I expect that's your problem, but hey, I could be wrong...