All the parts are doubled, some get replaced when launching a craft

[airelibre]

This has been happening for the last two or three versions I think, so it is not a new problem for me.

KSP 0.90 32bit

Problems (probably related):

a) In the VAB and SPH, the list of parts is duplicated. In previous version there was a whole set of parts, followed by the same set in the same order. In 0.90 the parts are now doubled up but with each part directly next to its double.

Some parts are replaced by other parts when launching a craft. Notably, all the elevons seem to turn into standard control surfaces. Also, this fuel tank (can't remember the names, sorry) which was originally the streamlined one turns into something else which doesn't match properly. When I revert to assembly, the part is still changed, so starting a flight seems to somehow change the part even in the original craft file.

Mods:

http://imgur.com/gNm7bgU

[Master Tao]

If you have steam, delete your KSP/GameData/Squad folder and and verify the integrity of the game cache with Steam. Otherwise, delete the same folder, and copy it back from a fresh install.

Several parts, namely the Mk 2 and Mk 3 space plane parts were moved, renamed, or recreated in the last couple of versions. ATM, you have both copies the old and new versions installed. You could delete them by hand, but it's probably not worth the effort.

[airelibre]

If you have steam, delete your KSP/GameData/Squad folder and and verify the integrity of the game cache with Steam. Otherwise, delete the same folder, and copy it back from a fresh install.

Several parts, namely the Mk 2 and Mk 3 space plane parts were moved, renamed, or recreated in the last couple of versions. ATM, you have both copies the old and new versions installed. You could delete them by hand, but it's probably not worth the effort.

Thanks, that did the trick. Any idea why this happened? It shouldn't have, right?

One more thing. I didn't check what was in my Squad folder before deleting it, and I think doing so has got rid of my custom flag. Is there anything else I should know about that I need to retrieve from the old folder?