Just a couple of quick thoughts . . .
When aligning the fence against the dogs, it is easy to have the fence very tight against 1 dog and just slightly less tight against the second one. To prevent that you could try taking 2 sheets of paper or Post-It Notes and sandwiching one between each of the 2 dogs and the fence. You will know that the fence identically (or as close as you'll ever get it) tight against the dogs by the ease with which you can pull the paper out. If the paper is tight between both then it's as good as it gets. If you can pull one out easily then that point is not as close as the other.
When cutting against the guide rail was the rail clamped down on the wood you were cutting and the table? If not, while it is not necessary to clamp the rail down, it is possible for it to move slightly.
In both of the above the differences would be slight, but then your measured differences out of square are very slight also.
I have chosen not to mess with dogs just for the above reasons. If I'm going to square up something it will be the fence to the guide rail. Same amount of time involved or less and the MFT/Fence is made for just that purpose. However, we all use the methods that get the best results for each of us, so whatever works. I'd pick one method and use it until you find that it creates problems with whatever you're making; then look for ways to improve.