Sources (from this event) say:

Lupe said Atlantic wanted him to sign a contract that would give them 25% of anything he makes from shows or deals with other companies like Nike or whatever.

He told them NO so they threatened him by not pushing any of his new songs on the radio or giving him money to make the videos (the I'm Beamin' video came out of his own pocket).

Also they basically don't like his music or the way Lupe put it 'They think I'm whack'. So Atlantic sent him hooks they wanted him to do (like Nothin' on You). He recorded them and sent them back but they didn't like them anymore and tried to have him change the hooks like 60 different times. In the end he had enough.

Shit like this get me tight but its interesting because his last album went Gold and both of his albums have received praise from fans all over. He was nominated for Grammy's for a reason.