This is the manager talking, rather than the engineer. This is a hardware problem, and it sounds as if you've already spent more time on trying to find a software sticking-plaster than is cost-effective.
Have you tried another brand of 16MHz clock oscillator? Farnell have heaps of alternative parts avaialble off the shelf in a variety of packages.
If the part you are using really does have a built-in source termination resistor - which does seem to be the most likely explanation of the flat spot on the clock waveform at Fpga1 - swapping to a different manufacturer might cure the problem.