Sorry, I swear I've tried searching half a dozen times, but to no avail.

I've put my mods into the folder with Cortex Command.

There are no errors on startup.

My mods don't appear in game.
(When I do a skirmish, the build menus don't include the objects from the mods)

Which folder, exactly, did you put them in?
As in the file path

Why does it matter exactly? They're in a sub-folder off of my desktop with the rest of the files.

The path is as follows:
C:\Users\Markonite2\Desktop\Stuff\Game Files\Cortex Command

Mods should be in Cortex's top directory, so you should have, for example, Data Realms/Cortex Command/AAL.rte.

That's the way I have it. Here's the file path when attempting to use a mod:

C:\Users\Markonite2\Desktop\Stuff\Game Files\Cortex Command\DarkStorm.rte

Do, by chance, have the registered version of Cortex Command?

Yes! I love Cortex Command forever! Full version kicks salad!

Oh god, you actually did say salad. I... I can't believe that. I had to turn of the censoring to make sure, and I... I don't know what to say.
On topic, I have no idea why it isn't working.

Maybe I should permanently migrate over to this forum from the dead one I'm on now.

On a more topographically correct note:

Can anybody help me?!

This could not possibly make any difference. Ever.

Anyway, a common problem is extraction bugginess.
So make a new folder elsewhere with the exact same name as the mod folder, Ctrl+X every file inside the mod folder to the new folder and delete the old folder. Now move the new folder into the game directory and try again. That might help.

Actually, I just tried again and I got the mod to work this time, now I only wish the other ones worked.
The entire base module expansion pack is in place, all the different parts separate like it says in the read me.

I want those base modules!

Besides that, I think the other mods will work from now on.
I've tried the folder re-create trick and it doesn't seem to effect my files.

Oh. I must have read it wrong when the UNREGISTERED VERSION said that REGISTERING would grant the ability to USE MODS.

So is there any reason BMCP 2.0 won't work on my game?
Is there a special way to install it?

You are referring to the "Modification Loading" text on exit? False advertising, probably forgotten after whatever late-night compilation Data did two or three builds ago. Try running your game in unregistered mode, cut out your registration information from settings.ini even, they still work fine.

EDIT: To actually answer the OP's question, which way are you trying to install it? Integrated or not? If not integrated, you should just be able to dump everything into your Cortex root. It's been a while since I tried it, but integrated is mostly the same but you have to copy/paste a whole lot of crap into base.rte/index.ini or something.

Non-integrated I guess.
What is the benefit of integrated?

I just want the objects to show up in the build menu during skirmishes.