We have fixed this bug in our code and this fix will be released as part of 5.7.0 at the end of this month. Moving modules also creates fewer changes so there will be less chance of conflicts.
If I remember correctly this bug has been fixed recently, so maybe it is fixed in 5.4.1, or it is in an upcoming release. It is harmless but annoying indeed :)
For what it's worth, I fixed it by changing the position of the modules according to the Sort Index's difference between "mine" and "theirs". You can see what position it is by double-clicking the change record of the module. If "mine" is at 11 and the other is at 10, moving the module one positon up does remove the change.
Hope this helps out those who won't be moving up a couple of versions for a while. :)
The ticket for this is high on our backlog now and I hope we can fix it in time for 5.8.0.