I have used Cortex since build 20, and I have not had this problem. Maybe that was b19?

18 was the first one with the demo, methinks.

Okay, this sounds familiar.

Q: Does the compressed file(s) for the mod(s) have 'rte' in the file name(s)?
E.g., modname.rte.zip
If so, that might be your problem.

The unzip utility I use (and the one that comes with XP) will make a folder named after the zip file, and then put the contents in that. If the zip file is already named after the rte file, then you can get TWO rte folders.

Example.
DarkStorm.rte.zip
When unzipped, I get a folder named DarkStorm.rte, which is named after the zip file, and inside of that is the actual DarkStorm.rte that was in the DarkStorm.rte.zip file.
So, I will end up with something like Cortex Command/DarkStorm.rte/DarkStorm.rte

Due to this, I keep my mods in a separate folder, unzip the file, copy/cut the 'actual' rte out of the 'fake' rte, and then paste it into the CC directory, then I delete the 'fake'/empty rte folder from of the mod storage folder.

Did you actually see the screenshot?

Not to offend you, but I already know that the .rte has to have the .zip file removed. It's just that it refuses to load anything even with modloader downloaded and saying they're all active mods.

I don't use the modloader, I do everything manually when it comes to plopping mods into CC, so I know basically nothing about modloader.

I did not see the screenshot.
I did not know the psd file you posted was the screenshot you mentioned. Heck, I had to google to find out what a psd file even was. (photoshop document? I don't have Adobe Photoshop...)
I don't have anything that 'actively' recognizes what a psd file is (properties said "opens with: unknown application"), luckily it seems quicktime picture viewer can open it.

Did you trim that screenshot much?
The base.rte and the CC exe are the only two vanilla things I see in it.

You have CC installed on XP, correct?
I have XP, but I don't have a Thinstall folder in my CC directory. I do have all the files, dummy.rte, coalition.rte, etc, in the main CC directory with the CC exe, but no Thinstall folder.

I tried to search for what Thinstall was on the forums, and on the CC wiki, but found nothing.
Curiosity and searching on Google spits out stuff about application virtualization (???) and USB apps.

I am totally at a loss to how that kind stuff even applies to CC...

Crazy Question: Do you happen to have CC installed on something other than a HDD?