Hi Pluto,
The simulation mode only depicts the actual cutpaths being traversed, and not any retractions to the Rapid Height or the rapids themselves. Only ramping and helical entry cuts are also depicted, but plunge entry cuts are not included. It sounds like a potential CNC controller situation, perhaps a work offset that's being triggered. What post-processor are you using?
Have you looked at the G-code output itself to see what's happening at the end of one operation and the beginning of another? I'd like to take a look at it if you could send it over to support@deftware.org :]
- Charlie