Ray:
Have you taken your code and made tight test loops in the code that access the clock interface and then looked at the waveforms on an oscilloscope?

If you have not done this then you do not have a full understanding of what could be wrong or where you may need to make additional corrections.

An embedded software programmer that is tasked with bringing up hardware should always have an oscilloscope at their disposal. To not have this is equivalent to sending the surgeon into the operating room in the full dark of night, without even the hint of a moon beam to light the way,,,to perform a major surgery without a clue of what part needs to be cut open.

Michael Karas