I can't say I've run into the issue you're describing on my Olympus yet, so hopefully it's not an issue with this brand! I plan on trying to do the stacking myself once I get a little more used to it, so I'll definitely need to find something that works for me. I use Linux, so that can make finding software a little more difficult!
How do you normally keep the camera steady when making all of your focus adjustments? I'm just using a fairly basic tripod at the moment, and even the slightest touch to change focus means I need to wait a second until everything settles.