[Alan Anderson]

Without seeing your code, it's hard to imagine what might be wrong. I can't quite follow your explanation of what you're trying to do. Can you show us what you're talking about so we can look it over for possible problems?

The comment about "normally" starting an encoder and reading it in the same loop doesn't seem right at all, but I'm not sure whether the problem is with the way you're describing it or whether you're actually doing what it sounds like.