I see the same problem here, on V5.3 I have also tested the new beta system 5.5B1 and the result is different as it says Preset 3610 is already loaded. So we'll have to look into that and obviously it won't be changed in 5.3 as we are moving on to a new system. I haven't used a sequence, meaning by that a single burst in which Bank change + Prog change are sent out together.
Now, the problem may be caused by the sequence of actions you describe, that is alternating the use of MIDI to remote bank and program changes AND changing the current DSP display with the Processor A/B front panel key. The whole thing is very unlikely to be done in real life use as the whole purpose of using MIDI w/banks and presets is to do changes from remote, thus without really touching the unit front panel. That is the reason nobody has found this bug before.
I'm sure you have stumbled into this while doing all your tests to solve the problem discussed at the beginning of this thread, thus almost accidentally.
One nifty feature in the bank change is that it allows to visualize on the display the bank. Using a fader that sends out CC #0 like I do here, scrolls thru the banks and changes the display from A to B or the opposite, according to which MIDI channel (1 or 2) the fader is working on. This happens only when the PROGRAM key is active.
Thanks for reporting this bug!