I've also found this in v3.6.0 although the behaviour is odd (I'm not using 3.6.1. yet due to the options save issue). I haven't played around with the compat. settings we set ours to 3.0.1 to match our report server engine.
You can add a group footer and add fields to it, then save. The group footer and the fields still appear in the designer but if you switch to XML view the groupFooter section is gone. And if you switch back to the designer the footer section and fields are still there but only temporarily - reload the report and they're gone.
This one really caught me off guard, I've been modifying a bunch of old reports and then noticed the loss during testing - ouch!
Only workaround I can conceive is to do all the work on the report, switch to XML view and copy the groupFooter section to the clipboard, save it and then open the report in some external editor and re-paste the section.
** Just checked another workaround - seems that if you save from XML view the groupFooter is not lost - only when saving from designer view.
+1 for a fix on this one soon please