Ehhm, i'm currently running 0.60.06a and having this problem. It crashes during profile switch and NMM doesn't seem to remember the profile setup and i get various error messages that this or that file isn't installed. That's just an outright lie because it damn sure IS installed in the profile i'm switching to, So far it has varied between:
"Failed to import the load order from: Profile Manager
Reason: BOSS_API_ERROR_FILE_NOT_FOUND: "ApachiiHair.esm" cannot be found!"
and also
"Failed to import the load order from: Profile Manager
Reason: BOSS_API_ERROR_FILE_NOT_FOUND: "RGMsAlchemistsCompendium.esp" cannot be found!"
And i have also encountered problems with missing plugins. The profile header claims i have for instance 133 plugins but when/if i'm able to switch to that profile it has only aprox 109 plugins installed or some such. And then the game CTD when i start. It shows the first start screen but CTD's before i get to the start options. (Continue, NEW game, LOAD, credits etc)
Any suggestions? I Dare not try to switch to my first Profile which was the one i'm in an ongoing campaign...
The main difference between the profiles are body types and associated clothings and armour. on profile 1 i run TBD /Touched by Dibella) and that's the one i haven't dared to switch back to yet. On prof 2 i run SevenBase and on prof 3 i actually have no body type yet. it's when i'm switching between 2 and 3 that these NMM crashes appear, obviously

I'm pretty certain it's something i've done wrong in the profile setup, but i'd like to know WHAT?