Well, I agree with mke - it can't be the POD, otherwise you wouldn't be able to write to RAM either. And with two devices showing the same issue, it's not very likely that both of the chips have bad Flash. Also - a secure chip should not be the problem either - because the BDM can erase a secure chip. Since only the Flash module itself appears to be having problems, that is why I suspected the timing.
I thought the processor expert only wanted to know the crystal frequency so that it could write the proper dividers in software for PLL, ADC, SCI, FLASH, etc. I'm not so sure that it has any relation to timing for the BDM and programming the Flash during development - but I could easily be wrong here. What happens if you open the Hiwave debugger and go to the ICD-12 drop down and select 'Set Communication Speed'. I doubt this will help because it is clearly already communicating. Perhaps someone else on this forum can confirm that it works with a non-4MHz crystal without changing any settings...
You are certain that all of the power pin traces on the board are correct, yes? And also the reset pin is connected to the BDM port? When I built mine, it just worked immediately with no fuss, and still works almost a year later. I've reprogrammed it hundreds of times without the slightest hint of a problem.