requesting extended stay bugged

[RAIST]

I was just in there tonight with my 5 stones. Went in with 60 minutes, added one stone to make it 108, still had my other 4 on me.

Sounds like you only had one stone on you, so it would only let you use that one stone. If you have more stones, the list is longer. You may have simply forgotten to get more stones from the NPC last time you were in town.

And that is how the stones have always worked, as I mentioned above. You can only request a total of 120 minutes per visit. You requested your saved 117 minutes when you first went in, leaving you with only 3 more minutes to request. When you used your stone, it capped out at the 120 minutes of requested time, giving you the balance of 3 minutes.

What you needed to do was exit the maw and come back in (resetting your request cap to 120 again), request your saved ~34 minutes, then use your remaining stone to tack on the 30 minutes (or more if you had the abyssites granting bonus minutes).

Edit: Details from the wiki on the main Abyssea page:

■The game makes a record of the total of how much Visitant time you have started an Abyssea run with, plus how much time you have received from time extension chests on your current visit. If this total is less than 120 minutes, you will be able to return to the Conflux Surveyor and extend your current Visitant status by exchanging more Traverser Stones.
■Warning: Any time granted by additional stones is added to the above total, which still may not exceed the initial starting value of 120 minutes. If adding a stone exceeds the 120 minute limit, any "overflow" time is lost. (Example: You start an Abyssea run with 80 minutes of Visitant time, get three 10-minute time extension chests which increases the total to 110 minutes, and decide to exchange another stone -- this stone will only grant you 10 minutes of Visitant time, regardless of how much time you had remaining.)