Maybe it is your soundcard. Not all soundcards work 100% with linux. and I think you would have to have DMA working with it to get good recordings. Playing directly and recording to storage take different amounts of processor time. Also, are you recording to a line in port on the card or a mic port. Line in and mic ports have different attenuation and might need a matching transformer or some other sort of level control. That is why higher end cards have both a mic and line in port.
feeding a Line Out to a Mic In just needs attentuator resistors, not a matching transformer. you can buy a mini-stereo-phone to mini-stereo-phone patch cable with these attenuators built in, designed to allow you to feed the line out from a CD player into a walkman style tape deck's mic input. The usual attenuator is 100K ohms in series, and 10k ohms in parallel . Note recording from a Mic Input will likely be noisier.
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