The PAL/GAL are programmable logic chips of very low complexity/capacity, often used to replace a bunch of discrete logic chips in bus address decoders and whatnot. Think of it as of tiny CPLD.

I don't know anything about that motherboard, but logically there is some optional feature that may be present or not, it is implemented using one (or more) of PAL or GAL chips, and you configure your motherboard with jumpers to tell the chipset that the feature is available or not. It seems you cannot make changes freely to JP40/41/42/44/45, those must reflect the presence of the chips implementing that feature.
I'd guess that the feature could be the bus mastering, allowing the card to initiate transactions on the bus. Without the additional PAL/GAL chips on the motherboard this possibility might be unavailable. Normal video cards wouldn't need it, only the disk controllers or some fast i/o cards could make use of it.

There was a manual on sale at Ebay that I ordered for this board.
I will know soon enough what those jumpers mean.