Spdif

I wasnt sure whether to put this under home entertainment system or not..... its not a home entertainment system so......

I spend quite a bit of time on the computer making music but have never recorded anything other than midi.

Im trying to record some new samples ive got on a mini disc. I did have a few problems with the input volumes but have sorted that.

Thing im getting glitches in the recordings on the computer.
I have the analog out on my md player going into the line in on my Audigy 2. This works fine, and if I swap the leads over sound from the comp goes into the md player fine.

But I get these little glitches... so idea is to transfer via digital leads.
I have optical 1 and 2 inputs on my md players, coax input and optical out.

I can have optical and coax input/outputs on my onboard spdif in. Ive enabled the spdif but it wont recognise signals from the md player. Nor will the md player recognise signals from the comp.

Basically the spdif isnt working on my comp.

Have I gotta remove my soundcard ? I tried disabling it in the device manager with no joy.

I really wanna use the digital cos the samples are just unacceptable if I use the analog outputs to get them on my comp.

The recording fine, the glitches only show up on the recording by the computer.
The quality im recording at too is far to high to be causing the glitches.

How do i get my spdif to work ???? And can I get it to work at the same time as my soundcard?
ie souncard outputs to the speakers and the spdif transfers to and from the MD player.

I havent got an amp I can run it through either, I broke it ages ago.

cheers for any help!!
Ill post the mix if I ever get it done..... it goes a peach!