OK. So I'm tryin to duplicate your situation. Here's what I did.

install V3.51

boot with 8 key held down – no problem.

install V4.01

boot w/no 8. when asked "clear setup ?" select  cancel. no problem.

boot again with 8 – no problem.

Go to Setup/Externals/EXT1 and Set for "Midi Single" then CC#88,

then go to Setup/Externals/EXT2 set for "Midi Single" and CC#89

Then go to Setup/MIDI switch the midi channel from OMNI(default) to midi channel 2

Then got back to EXT 1 and 2 and set the base midi channel to 0 instead of -1

Then go to Setup/Externals/FXA bypass and set for EXT1, trigger mode to On/OFF and Sense to "reversed"

Then go to Setup/Externals/FXB bypass and set for EXT2, trigger mode to On/OFF and Sense to "reversed"

Load Program 100 and reboot. No problem.

So, I don't think this is a bug – more likely a hardware issue. There are some self tests you can run. You'll have to reboot with the 8 key afterwards.

1) Power cycle with 5 key held down. Release it immediately you see "Test All."

2) Type 1,0,6,ENT.  It should show "106 NV Ram".

3) Hit TAP. Let it run for a few minutes. You should see P=xx E=0 T=0.  If E or T are not 0, it is a fail.

4) Hit TAP again to stop. Turn wheel 1 click right to show "107 Entire NV Ram."

5) Hit TAP. Let it run for a few minutes. You should see P=xx E=0 T=0.  If E or T are not 0, it is a fail.

If either of these tests fail you have a definite hardware fault.

If they pass, get the unit back to a good state, and leave it powered down for a few days. If you then get an error when you power up, it is probably the battery or holder, but could also be power-down circuitry.

Try the above, and let me know ….