Sound Check is a volume normalization algorithm built into iTunes and iPod. Sound Check normalizes based on the loudest audio sample in each track. iGain uses the Replaygain algorithm to normalize based on the average perceived volume of each track. For this reason we believe iGain produces superior results.
iTunes keeps track of the maximum volume and Sound Check adjustment in its proprietary iTunNorm file tag. iGain does not read or write this tag. If you enable Sound Check on songs that have been processed by iGain, they will not play back at the expected volume.
For this reason, always disable Sound Check, both in iTunes and iPod, when using iGain.