is 'accepted' status only temporary for whichever faction your working for?

Are you doing anything that would upset NCR? like killing or stealing.

no.

but I am losing karma in places unrelated to the NCR. (stealing)

not only that, but my vilified status with the legion is also being reset.

Do you have jury rigging?

If so there is another thread that might explain it. http://www.gamesas.com/index.php?/topic/1152571-half-my-reputations-have-disappeared/

If you are wearing ncr armor then everytime you put it on your rep goes to nuetral but if you keep it off it stays at what it should be

Havent got jury rigging.

could it be that ive unequipped my NCR armour several times?

Yes faction disguises would hide your real reputation while you wear them