Thanks guys for the comments. To answer some questions, there are a couple of things that changed since last year when I didn't have this problem.
I increased the angle of the saddle and lowered the saddle to compensate. I think I also adjusted the saddle position so that my knee is lined with the middle of the cleat when the pedal is at 90 degrees.
Result: no more sore butt and I can finally keep going for long distance no problem until I get that damn knee pain.
I am training much more seriously and I might be stressing a bit more the knee joints so that might explain why... cleat position was also modified. Can't seem to find the right set-up. I always end up with something not quite perfect...
The physiotherapist suggestion is probably the best. I hope I'll find solution to my problem. Will look for some one who has some experience with cyclist.
I live in montreal if by chance anybody know some one around there, let me know!