OK where are the woodworkers when you need them? First why would you have to grain fill pine it has no grain to fill???? RGman thanks for a knowledgeable response though brief.
Have you ever stained pine, well pine has soft and hard areas so it stains unevenly and is probably is the reason you are having sanding issues. You must have areas of the board which are soft, the hard soft lines generally follow the grain in my experience but it may also be a random pattern. No matter what you use the more you sand the worse it will get. Usually if I use pine (certianly not for guitar work) I havent had issues using a random orbit sander. Some pine could be really bad and it sounds like your problem. Old boards can be worse than newer wood because pine does not harden with age. if you have ever seen an old worn pine floor board, it looks wave like, because the softer areas wear faster. I have no solution other than to try a scraper blade on the hard areas (High spots) get it as flat as possible then sand lightly or scrap the piece and start again. Other options would require more expensive sanding solutions such as a thickness sander.
My personnel opinion (please read that again) is of you want a cheap wood to use on a guitar (I can see no other reason for using pine), buy Poplar instead, Its almost the same price and as a guitar wood will provide a predictable outcome.
+1 on Woodenspokes thoughts. Pine is a funny type of wood depending on the type. Yellow, hard, northern, lodgepole/western, they have many similarities and differences. But the short of it is very soft with hard grain lines. Not good for sanding. Sapwood is the mostly likely obtained now days no matter what subspecies, unless specified for flooring. So , I suggest you live with it, fill it, then coat it and level the clear coat or best, choose something else.
Yep not the answer you wanted to hear but that's the nuts of it.
MK