The problem isn't a sync issue, it's a pointing issue. A command is sent to the mount to move to a position and the position it reaches isn't the same. In many cases this can be seen without looking at the sky because the position the mount reports it has reached is different to the position it was sent to.
Frank is suggesting that this should be handed in the application - SGP. I'm afraid I disagree, I think that mount issues should be resolved by the mount manufacturers.
I think that supporting mount issues in a application is a recipe for disaster because it's a support nightmare. It would be like the DSLR support nightmare again. Some mounts may be OK, applying a consistent offset to the slew command would work but with some it wouldn't. Trying to support this for free, by email and forum, will be immensely difficult and hugely frustrating.
I wouldn't touch it with a barge pole, not even for money.
When you get down to it the errors that are being seen are tiny, something like an arc minute. It looks large because it's in pixels and that's minute. As I've said I would make the default limit something like an arc minute, even if expressed as pixels.
Chris