Are you serious ? You also do have the same issue with the Arpeggiator ? We're damned lol ! I tried your trick with the midi cable but unfortunately there's no change.
I can only use the Arp with an external clock source (you too ?) and it's not the "clock in" jack, i've replaced with a new one but nothing's changed.
It's not the 3340 used as LFO, indeed i don't have any problems with the waveforms when i use the LFO section.
Do you really beleive i should reset the CPU ? Hahaha, no i won't, i'm too scared, frankly
Anyway, here is what i got from a very nice guy (Jareth from Synthpro) about this issue on the internet, maybe it could help :
Take careHere is the signal flow for clock output to the digital board: Clock signal comes off the LFO through S21-3 on common analog and goes to S55-3 on DMUX, (DMUX is used as a jumper only from a ribbon to a wire so all passive).
The signal from S55-3 comes out of P517-1 to the clock Jack. When you plug a ext clock source in, it breaks the signal coming from P517-1 and feeds the ext signal from the jack to P42-5. Based on your symptoms you do not have any issues from the jack to the digital board but could be either a problem at S21 to S55 or from S55 to P517.