I am on HW 2.7 with SYS 1.50 v1.6 and GCC APP v1.29. I have not flashed my FPGA as it came stock with 2.61 (All the HW 2.7s do).
You are absolutely right in your description of the problem. Though that is not the only time I get refresh issues, it is certainly the most pronounced. 200uS time-base is completely unusable for me. This is not the case with the stock SYS/APP or with the stock SYS and Gabonator’s APP.