poppping would'nt be the gain.. unless your hearing the pop sound on louder output. If its popping in low volume I would steer towards weak connection either in low input(s) RCA's or the output voltage is lower than amps min requirments. Remember that headphone outs (ipod, PC, in general usually have >0.4v max output. I would start @ looking at your amplifiers specs and see if it can handle very low input.. A perfect match would be min input range of 0.2--8V, if yours is 2v min as most.. then I would suggest a line driver or connecting an Ipod and see if the problem persists. This can help eliminate the PC end so you have a general idea of where to start the troubleshooting. if it srtill pops is amp or wires if it disapears then its the PC outs. Hope this helps.
Did it.. Done it... now I got to keep the neighbors kids away!!