i can see sseveral possible causes.
-There is dust/grease/filth in your down microswitch, it keeps the plunging part up and it doesn’t triger until it has been forced out of the sticky position and then it works properly. not very likely considering the symptoms since on a Sanwa JLF-TP you readily apply a lot of strengh with the stick on the microswitch plunger, anyway cost for replacement is around 3$ shipping included forget about trying to clean it it is a non viable solution on the long run and not worth the hassle considering the cost of a replacement.
-your down microswitch is worn, you have to replace it, should have happened so early in the life time of the switch but… shit happens cost for replacement is around 3$ shipping included. it is the most likely.
-the harness wire is damaged somewhere around the line, unlikely given the symptoms unless it somehow managed to get close to the stick and gets moves when you operate it, which in turns changes the quality of the contact.
-you pcb is fucked, not very likely to happen ever those things usually last a decade.
unmount your stuff
plug it in as for normal use.
use a wire to short the NO labeled leg (soldered to the stick PCB) of the down command microswitch, (it is the one at the top of the stick), with the ground leg (it is the one soldered to the outer circuit on the stick PCB.
if it works it probably is worth unmounting everything and get a closer look at that microswitch.
if it doesn’t repeat the operation on the other side of the harness, short between ground and ‘down’ line on the TE main PCB.
if it works then it has something to do with the harness, check it for signs of cuts or plying, chek that it is correctly soldered to the master PCB.
if it doesn’t work, double check everything before concluding that the pcb is faulty.
My money is on a stick side problem though, problem on the microswitch could not be obvious or repeatable mesurable at will, take advantage of everything unmounted to clean the dust on all parts, mount everything back together and give it a try, if the problem arises again, get a new switch, remove the old one and replace it si cheap but you will need a soldering equipement to do that