I had a similar question because I was also applying from a (Canadian) masters program. There was an extra complication that the Canadian schools I was at didn't use the 4.0 GPA system (we got percentages). When I contacted the graduate admissions secretary, they said to just send the transcript and the school will decide how they want to calculate (and in my case, convert) the averages.
Sometimes by default, the application says the "last 60 hours of undergrad" but they would probably want to include your Masters work in there (but most people don't have one). I'm not on any grad committees, but if it were me, I would fill in my GPA from the most recent 60 credit-hours (starting from Masters) and attach a note that I did this (usually there is a box for this on the last page). They will get the full transcripts and if they don't agree with how I did it, they can calculate it the way they want!