are you using SCSI? As I recall the CD player in OS3.9 has a problem with the GURU-ROM if you are using an A2091 card or a GVP card.
Also, not all of the CD Players on Aminet worked for me, so try different ones.
Are you configuring the CD player correctly to recognise your IDE or SCSI device?
I use a little CD player from Aminet to play my CD through my Repulse card. I think it's called TinyCD or something.
Also, make sure the input you are using on the Repulse card is not muted in the Repulse PREFs.
Oh....and lastly, make sure you are monitoring the audio coming out of the Repulse, and not out of the Paula (i.e. the Amiga's L & R audio sockets). The CD doesn't play through the Paula.