I had the problems described in this thread on my list to review, and I've just spotted a firmware issue that could explain them. The fix will be in firmware 1.20beta9. Anyone still having problems with commands in tool change files not being executed properly, please try that version when I release it.
EDIT: the workaround for now is: if any of your tpre, tpost or tfree files contains a movement command, add command M400 at the end of that file.