Hmmmm, that IS strange. I have a Pokeys setup basically the same, 2 analog pots, one for FRO, one for SRO, and they both work fine with brains.
What you're saying is, it works great AFTER 30 seconds? I suppose I've never tried it within only 30 seconds after starting Mach3. By the time I load a program, 30 seconds has elapsed. But I'll try it and see.
What brain are you actually using? Could you post it here, or point us to it, for us to look at?