I've used Geckos for years, and never had a problem. No experience with Copleys. However, I fail to see the connection between PWM frequency and encoder counts - they're pretty much unrelated. I don't even know what the PWM rate for the Geckos is, but I run mine with 20,000 PPR on two axes, 20,320 on a third, and 96,000 on a fourth. All work just fine. I think perhaps you're imagining a problem where none exists.
Regards,
Ray L.