What version of Sins do you have? I remember old versions of Sins needed ALL of the game files in the mod folder even if they weren't altered. I don't remember if they later changed it to bring it in line with Entrenchment/Diplomacy.

Thanks for the fast answers.

But do you mean only the complete GameInfo folder, or also the texture, sound and other (non addon) folders and files?

It does make a difference, because I want to send this mini-mod (replacing all blob lasers with beam-effects if anyone cares) to a friend, so the smaller the better. The GameInfo is just 1.27 MB, so no problem to send. The Sound and Texture folders on the other hand are more than 200 MB and 1 GB big.

But luckily it is enough to only copy the GameInfo folder, which makes matters easier.

Thanks again for the help.

VERSION? 

What version is the game at and where did you get the reference files? All modding questions need to start with this most basic info please.

The Org Sins needs all the Reference files, not textures or sounds. Basically all the files that Ent and Dip manifest files list because Org Sins does not use manifests.

As I already wrote in the post directly above the one you answered to, I took the files from the game's root folder ([...]\Stardock Games\Sins of a Solar Empire\GameInfo). Version is 1.191 of the original. But why would that matter for files being completely ignored?

And I found the problem. It is (again) something that works fine wtih the addons, but makes trouble for the original. Inside the GameInfo folder I had a Backup folder, with copies of the capitalship files in easy reach. For some reason the game loaded the files in that subfolder, instead of the ones in the actual GameInfo folder. Moving the Backup folder somewhere else resolved the issue.

When I did something similar for Entrenchment and Diplo, it worked just fine (with the files in the Backup folder being ignored), so I didn't expect that to be the cause.