If the CB-Emu team have been able to accurately emulate the clock at 32 MHz. Then unless you are playing the settings for fun entertainment, when using a times 3 setting, ponder should be turned off for both computers, or you play a CB-Emu level where the CB computer emulation does not handicap the other computers pondering time, which of course would emulate a higher MHz as for example 96 Mhz if using 90 seconds (Times 3) versus 30 seconds.
I think this why we are all confused not knowing exactly the settings.