This is a very minor change from V1.0.8. The default value of REFCLOCKGHZ in rccerun was 1.0 ... RCCE_V1.0.9 changes it to 0.533.
This value doesn't set any clock or affect the operation of the chip in any way. It's used just for timing measurements. For example, if you set it to a very high value, you'll get very good performance measurements, but your actual performance will not change. When you train your SCC system, the default clock is 0.533 MHz. Now rccerun has that default value.
The value that RCCE uses to measure performance is overridden by the -clock switch on the rccerun invocation line. If you don't use the -clock switch, you get the default value in rccerun.in.