We experienced the same problem during our install took a couple days to solve but now owrks great. We found that the problem seemed to occur more when using the same type of fax machine on each side and they transmitted at a higher speed. In the end the problem was solved by installing the latest at the time - vg248 ios and changing some setting.
Here is what we have software 1.2(1) and dsp 3.6(20x)
Fax relay enabled on call manager gateway port. Default settings for speed, relay etc on vg248.
Feel free to email me if you would like to compare settings.