Well I managed to solve my problem. It was a problem in the top level entity again. I forgot to set the value of the pixel_clk_reset for the video in decoder as low, since I'm not using it. I also added a PLL in order to give a 25MHz clock to both the camera and the VGA, though I don't think this is a necessity. The solution/source files are in this thread:
http://www.alteraforum.com/forum/showthread.php?t=45407&p=187771&posted=1#post187771 The next step is to fix the exposure, frame rate and resolution since the result of the camera is poor for now. It should be easy to fix it from QSYS though.
I'm starting to think the UP subforum has been abandoned by people that can help haha.
Ammar