i've had this happen as well on my edge. 9 out of 10times, it's just easier to do what you're doing. home it, manually rewind the roll, insert next color and repeat until its done.
it could be something as simple as the punch being just slightly off. it could be the backer getting worn out from the multiple passes. it could be ..... by the time you figure out what it is that's causing the problem, you could have had the job run the other way.
so unless this is happening all the time, it's not a big concern.