It sounds like you've got a fairly large part, so that when you change the X-Y origin it is pushed over the edge. If your Z range is small, switching to a center in the middle of the part rather than the top will do the same thing. Check the overall dimensions of the part you're trying to make, and the dimensions you've input as the machine's limits, and position the part so it fits.
Is your machine stopping on each of those M-codes? If not, just ignore them. If so, you can either edit your post to keep them from being added (ask Flashcut for help with that if you can't figure it out) or bring the program into Notepad and use the search-and-destroy function to edit them out.