My bet is your Xylotex is overheating. I just had this same problem about a week ago. I'd run a huge job and about 30-40 minutes into it things would get messed up. Sometimes I'd lose steps and a few times my X and Y wouldn't be able to go in one direction. It took a bit to figure out but the fan that blows on the Xylotex board had shifted and wasn't blowing right on them. So what I did is laid the fan right on top of the heat sinks and now everything runs great. In fact I think I can run faster (I have no proof of this but it just feels like I can push things a bit more) Is your Xylotex in a box and what kind of cooling do you have for it?
Take it easy.
Jay (www.cncjay.com)