with S/PDIF input, the sample rate is detected automatically. there is no way around that fact.
a few things. with 24 bit, you'll never be able to get 3+ hours in a single file. at 24 bit, 48kHz, you'll hit the 2 GB file size limit around 2 hours. at 24/96, you'll hit 2 GB around 1 hour into the recording. These is the reason why so many of us want M-Audio to implement a feature where it'll automatically start a new file when the 2 GB limit is reached.
It seems like the "Rec Time Available" is being reported to you, assuming a sample rate of 96kHz in both cases. so, now, instead of basing this off of what it says when you hit "Rec Time Available", why don't you feed it an S/PDIF stream, start a recording, and see how much time is left on the countdown at the start of the file. if it's around 2 hours and you're giving it 24/48, all is fine. Some people have reported problems with the total time that it counts down from. one thing to try, that seems to work for some people, is to record a short file, just a few seconds. and save it, and start a new one. this second file starts the countdown from where it should. This is a small bug that M-Audio is aware of. Still, it wouldn't hurt to let them know what you are experiencing. Hopefully this issue will be resolved with a future firmware update.