Ok firstly, using steam achievement manager does not work. If you used it then you'll need to lock the achievements again and unlock them legitimately. This is because you need to set certain flags, which also happen to unlock the achievements, but having the achievements does not mean having the flags. Because of this I think it's misleading to say you need the achievements to unlock paint at the right time.

Next let's make sure you're not just doing something wrong and missing a paint line. In a cube any% run you get the following lines:
Start a new game
Unlock an item
Solve a puzzle requiring an item
Read a QR Code
Listen to an audio log
If you're missing any of these you won't get paint. The most important one here is read a QR, it's the only one that doesn't save the game, so if you reset right afterwards it doesn't count, you need to get a new checkpoint first. If you do it like Azo does it in his tutorial you should be fine though.

If nothing's worked so far it means there's something going on with your save file. If you unlocked the achievements on a different computer to the one you're trying on now, and you don't have steam cloud on, then the save with the right flags would not be transferred, so you obviously won't get paint. The fix for this would be to turn on steam cloud or copy the files manually (they are in "[main steam directory]\userdata\[your steam id]\257510\remote"). 

One last thing that might have happened is just that you deleted the save manually after getting the achievements. You'll know if you did this and the only real fix to to unlock them again.

While messing around with Portal 2 I noticed that anything higher than 2x AA kills fps if looking at a portal while OBS is open. I also always open task manager and give hl2.exe a higher cpu priority. That pretty much fixed 99% of all fps drops I had.

Portal

The Talos Principle

Paint refuses to Spawn

SourceUnpack FPS Issue