I've got a My Games folder, but there is no Ironclad Games folder there. The only folders I have there are Civilization 4 folders. Should I create one?
The closest thing I've got to what you describe is located at C:\Users\Lloyd\AppData\Local\Ironclad Games\Sins of a Solar Empire - but there's no Rebellion folder there either. There are three mod folders there though. Mods-Diplomacy v1.34 (Which only contains one file, EnabledMods.txt), Mods-Entrenchment v1.053 (Which only contains one file, EnabledMods.txt), and Mods-v1.193 (Which is empty).
The other related folder I have is C:\Program Files (x86)\Stardock Games\Sins of a Solar Empire - Rebellion. But that folder only has five files in it; header_logo.png, inifix.cmd, sinsrebel.html, ssed.exe, and UninstHelper.exe.
I can't find any other traces of Rebellion on my computer.
*Edit - I had a look at the mod destination as you suggested. It does say it's supposed to be in the My Games folder. i guess the game hasn't created a folder there for some reason.
*Edit the second - ah, i've found it now. Idiot me was looking in the wrong place. I was looking in C:\Users\Lloyd\My Games instead of C:\Users\Lloyd\My Documents\My Games. Oops.