5 year holds poop and refuses to use the toilet

I have a 5 year daughter who over the last year has held her poop for up to six weeks at a time.  I know it hurts by the time she can't hold it anymore.  We have talked to our doctor and he has given us medication to get things moving.  He told us it will take some time to get her retrained.  When she should be back to normal, she totally refuses to sit on the toilet but does it in her pants.  There have been a lot of changes going on this past year.  Dad being laid off and being stay home dad for several months.  Mom's job moved to another county so I leave earlier and get home later.  She started school in August and dad finally went back to work.  In November, dad has now started better job on different shift and will return to regular shift in couple of months.  So, a lot of changes.  We have tried to make things at home as normal as possible.  For us, the frustrating part is we go from one extreme of her holding it for long periods of time to another of having 2-3 accidents per day.  We have talked to her until we where blue in the face and are now trying to disciple her for doing it in her pants but that doesn't seem to be working either.  We want to try and understand why this is going on.  Any suggestions would be greatly appreciated.