If both line level inputs that you'll be connecting to have been used equally, you should get equal results.
One of my friends was using a dvd player to listen to CD's. After taking his system apart, he switched the output of his DVD player into the input of his receiver labled "DVD". In the past, he had used the "CD" input.
When he started listening to the system again, he found that it sounded very different and not for the better. He then disconnected the DVD player from the DVD input on the receiver and hooked it back up to the CD input. The sound was back to normal. While he was skeptical of the results, further testing with my brother swapping the cables into the two different input jacks showed that there was a discernable difference.
The only thing that we can figure is that due to lack of signal flowing through the internal jacks and wiring, the sound was different due to a lack of break-in from extremely limited use. As such, i would verify that the player sounds the same between both inputs using one set of cables prior to counting on getting identical results. Sean
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