Hello Stoney,
I no expert on this but here's my two cents worth...
I have an iAmp600, and I think the pre-amp input sections are similar. The active input has a fairly low input impedance, it's 10K ohms. This is probably what Gary was referring to, and might explain why you have to crank the input gain to get an acceptable level. Most active instruments work OK using the passive input and the pad. Passive basses (e.g. stock P-Bass) work best with the passive input (more gain, 1Meg ohm input impedance). I think the 10k impedance just may be to low for some onboard preamps to drive. In general, If the amplifier's input impedance is too low, you could experience loss of level, changes in frequency response and/or distortion from the source device.
EA mentions the input impedance in their spec sheet, but they don't mention how it might affect the instruments we use with their amps.
Thanks,
nate.