I don't know if that's a software issue or not, but several seconds does seem a bit long. It also depends on what algorithm you're using. For instance, if you change from a fast Rotary to a slow Rotary, the change in speed occurs more gradually than if changing from a slow Chorus to a fast Chorus. That's by design. Because a mechanical rotary speaker takes longer to speed up or slow down, this behavior is duplicated in the MF Rotary algorithm.
What algorithm and or preset are you using? Knowing this may help answer your question more accurately.
Anyway, I'd suggest updating to the latest available software update. There are a lot of new features as well as some general improvements. You can find details and instructions here… http://eventide.com/Home/Eventide/AudioDivision/Products/StompBoxes/ModFactorUpdate.aspx