Recurring both 32/64 Tahr/Xenial, when I first restart JWM per boot, I lose my custom second tray.
Without understanding the cause, here is a hack fix:
Rename the custom from .jwmrc-tray2
Add the default 2nd tray in JWMDesk
Replace the default tray with the custom
Restart JWM
It works but is laborious for having to recreate the default tray in JWMDesk.
The real fix is understanding the cause, but without, automation is much easier with a cli option.