So in my current adventure, the PCs have been away from port for five months now and I'm looking at the possibility of thier supplies running a bit low. In the rulebook the guideline is that a ship will have about six months worth of supplies aboard. But does that mean six months real-time or warp-time? I would assume warp-time (In which case the PCs have only concievably used about two months of supplies - I kept track). What do you guys think?

I think you are correct. People don't eat more food/ consume more oxygen/ use up more fuel just because they are in warp transit. It is the time felt by the passengers that count. This can go both ways: being caught in a warp storm and getting stuck for six months and when they finally break free, only a week has passed in realtime.

Well, the Warp Time is the actual time experienced by the crew. So go with that

It's supplies for six months apparent time for the crew. They experience time spent in the warp 'normally' regardless of how long actually passes in real space.

Like others said it's subjective time not real time.

But if you want a plot about supplies running low, go for it.

Food or water tanks can become contaminated, accidents happen (BOOM! water supply leaks into space), as does sabatouge. Heck maybe crewman Jones just cracked up and vented your space fuel into space.

You've also got possibilities from the mismanagement of supplies. Stocks of food and perishable goods turn out to be lower than they should. Is a crooked supply officer skimming supplies from the vaults and selling them to the lower decks? Have mutants from the bilge decks found an abandoned ventilator shaft connecting their warrens to the supply deck, taking advantage of this back door access? Did a rating adopt a harmless fuzzy cooing thing he found on shore leave, and did that thing breed and breed and breed, then get into the supply decks and scoff all the xenocultured grain?

When supplies get tight other adventures will suggest themselves. Cannibalism breaking out on the lower decks, work crews raiding other work crews for water, drawing lots to see who among the crew will be placed in stasis to conserve supplies with no guarantee they will ever be revived.