Curious?
Follow Joe's recommendations.
It might help if you understand how that jig and all box joint jigs work.
The pin (pin plates or peg fingers as Joe calls them) aligns and indexes the board for each cut. It must must be set to the exact width of the dado cut (not what you think the cut should be). The spacing between the blade and pin (or nearest pin plate) sets the width of each finger and should be set exactly the same as the pin (pin plate) width. Anything else will affect your cut.
The pin size (pin plate spacing- outside measurement) should be set to the width of the dado cut FIRST. Cut a notch in a scrap board with the blade blade set for your intended finger size. Place the dado over the pin plates and adjust their spacing until they are snug against the sides of the dado. There should be zero slop but they should not be too tight so they bind, or worse bend. Do this each time you get ready to cut box joints in case the dado width is slightly off for whatever reason. DON'T try to set this spacing with calipers and don't assume because you are using trimmers and chippers that are "supposed to yield a 1/4" wide dado that they will actually cut a dado that size. Many dado sets cut under-size from the published thickness and require the use of shims.
Once the pin plate spacing is set, lock it. You should not need to adjust it again. Now set the blade to pin distance. Unless you have the new revolutionary jig due on the market later this year :icon_thum you will need to use calipers and/or the trial and error method to set this spacing. This spacing controls the width and fit of the fingers and should be exactly the same as the width of the pins. Too small and the fingers will be too narrow and too loose, too big and the fingers will be too wide and too tight (may not fit at all.) Once this spacing is set make some trial and error cuts. If the fingers fit too loose, increase this spacing very very slightly (partial turn of the knob), if they are too tight, reduce this distance very very slightly.
Technically you should not have the problem of continuously decreasing pin spacing. Whatever the spacing is it should be uniform acreoss the width of the board. The spacing may be different between the two boards but not obvious until you reach the edge. This situation usually results if you change settings before cutting the second board. But it can also be caused by a number of issues- the position of the jig miter bar or miter gauge mount is slipping, any of the other settings are slipping, or if your spacings are not set properly and the stock/notches can move back and forth over the plates. In that case the the spacing of fingers can vary if you register one notch against the left plate and the next one against the right plate. I suspect your settings are changing or they are not set properly and you are not being careful when indexing the boards.
This is so much easier to demonstrate than explain. Good luck.