Problems loading mods, ending up with missing parts! Am I doing something wrong?

[MeepZero]

So I downloaded MechJeb, AIES, and KW Rocketry because they looked like fun packs to play with. When I load up either AIES or KW Rocketry I'm noticing that I'm missing a bunch of parts from both packs. I'm taking the files and placing them in the Game Data folder so their mod title is on the top level, with all of their associated content within those mod title folders.

Is this a known issue with MechJeb / KSP or am I doing something wrong here?

[Fel]

if you alt-tab while the game is loading parts, it will fail to load some parts or something :S

[EmissionGeneration]

I've noticed not all Mods yet are meant to go into the GameData Folder [Recent Releases, not old Versions] If I generally have problems with the GameData then I stick them in the old traditional way and they 99% of the time work out fine after that. As I do not use KW Rocketry and AIES, I can't say for those.