Try this; turn the volume all the way up to listen to the background noise of the cd and the analog. If you get a lot of hiss in the analog, it may be an indication that there is something going on with your phono stage or interface between cartridge and phono. It won't give you absolute results, but it may lead to electronics and wiring as oppossed to tracking.
If you do get a considerable amount of hiss, substantailly more than the cd rig, try some different ic's and different connections to see if it changes. Try to eliminate as much as you can in order to isolate the anomoly, no matter how simple it sounds. I would evan unplug my ic's from the back of my cd and plug them into the phono and visa versa, just to see if it is the sound of the ic's I'm hearing or something in the pre-amp that is different. It's hard to tell from here if there is something wrong, there is just a synergistic mismatch of components, or if it's a matter of taste. From there, you might have a better shot at finding out which it is.
If you do get a considerable amount of hiss, substantailly more than the cd rig, try some different ic's and different connections to see if it changes. Try to eliminate as much as you can in order to isolate the anomoly, no matter how simple it sounds. I would evan unplug my ic's from the back of my cd and plug them into the phono and visa versa, just to see if it is the sound of the ic's I'm hearing or something in the pre-amp that is different. It's hard to tell from here if there is something wrong, there is just a synergistic mismatch of components, or if it's a matter of taste. From there, you might have a better shot at finding out which it is.