Oh yeah, they did move X-files for him, or atleast he had a big part in it.
Well according to an article i read on Zap2it.com, (maybe it's the same) he said he wasn't returning because he felt Mulder was just a secondary side story. He wasn't happy with that because he said X-files is about Scully and Mulder, which is partly true.
But first, X-files is also about weird people and crimes, lol.
In addition, the reason why Mulder became a secondary side story, was because he left! And also, i don't think his storyline is that secondary...i mean, i don't remember too many episodes where there was NO mention of mulder.
BTW, i think the money issue he was talking about was about syndication rights and stuff. I think he was complaining he wasn't getting enough.