Hey CJE, no worries, happy to help. My take/guess so far, given your symptoms, is there is some issue with the internal clock which is associated with the chorus (used for delay time/modulation frequency) but MJMP knows way more than I do about the internal workings of the circuit and can hopefully help sort it out.
Meantime, some things to try/think about to understand it better. So if you don't notice the ticking when the gate is on, it may mean the gate is turning off the signal and masking it out. Thus a temp fix is use the gate on all programs but adjust the threshold really low, start at 0 and just increase until you can't hear the ticking. It wont hurt to have the gate on every patch and at really low threshold levels, it shouldn't choke you signal at all. The gate shouldn't need a clock so I don't think the issue has anything to do with the gate as such.
What version is your EPROM? last one made was v1.41. The version is displayed when you turn the MP-2 on but you can also check the EPROM, take off the lid, with the front of the unit toward you, the EPROM is located in the right hand front corner area and should have a sticker on it with the version. But I don't think it's an EPROM issue

. You can (gently) remove the EPROM chip and re-insert it (careful not to bend the pins/legs) which will cause a reboot load and diagnostic check when you turn the unit back on. I've attached the MP-1 EPROM install notes for reference, It's in much the same place in the MP-2 and the instructions for removing and replacing the EPROM are the same.
The EPROM (erasable programmable read-only memory) is a chip which has been programmed with the code (assembler/machine code) that programs the MP-2s CPU to control the units digital circuits. It also stores the factory program settings which get loaded into the internal RAM chip and/or read/referenced in "preset" mode.
ADA call it a software update, which makes sense as you can change the code (reprogram the EPROM), though not for the feint hearted. As I said before, the MP-2 v1.41 change was more a fix for the slow program change speed that an upgrade as such. Where the MP-1 v2.0 & 2.01 added more factory presents and included additional sysex functionality.
If you have an older version EPROM (i.e. not v1.41) and/or you want to be absolutely sure your EPROM is programmed properly you can buy a v1.41 EPROM from MJMP and replace it (http://www.marshalljmpmodshop.net/miscellaneous_parts_and_replacement_tubes.htm).