Thanks a lot for your help.
I have some issues downloading the Telestream Episode Pro, so I couldn't tested it. Anyway it's so expensive than even if works I'm no going to be able to use it.
So far what is working better but not perfect is a software called AVS Video converter. It can read all my files even those ones that are causing crashes in Mpeg Streamclip, Quicktime Pro and Compressor.
To be honest I couldn't find a pattern or a reason why some files can be exported with these software are why other don't. All have been recorder with the same system, just the size vary.
ideo converter
The AVS Video converter let me recompress the files in Jpeg sequences at 1fps, so I get an speed up version 30 times faster than the original. After that I open the image sequence with Quicktime pro and then save it as a .mov . it's a pain in the butt, but is working.
I'm not an expert in compression techniques but I've being involved in the Vfx Industry for the last 20 years as Digital Artist and VFX Supervisor. This is my work
http://www.martinlazaro.com
My problem was due to the fact that I couldn't use any other system to record my project except the XM-DVR Pro. This footage was extremely long, 800 hours recorded in a very harsh environment. And this system doesn't have any settings for different compression.
I hope I can finish my project and post it here for you guys.
Thanks again.