The mechanism used on the PicoScope 5000 series for external triggering differs subtly from the mechanism used on the PicoScope 6000C/D series. Replicating the signals that you used in your tests, the 6403D has a lower trigger limit below which the triggers reduce or stop. For the units we have in our department the lower limit for reliable triggering is in the region of 6mV for an input signal (1MHz sinewave, modulated 100% with 1Hz sinewave) of 200mV p-p, while there is no lower limit for the 5204 down to zero volts.
So, in order to guarantee triggering in persistance mode for your PicoScope 6402D, we would recommend that you increase the trigger level to maintain reliable triggering comparative to what you have been used to seeing in your PicoScope 5204. Alternatively you could send the sync into channel B and trigger off of that to lose the level restriction.