I have reset the C3 just in case.
I have also done the following using FreeRip Basic:
Ripped a CD to FLAC format - All tracks play fine with no issues or pops between tracks.
Ripped a CD to MP3 Format (although the max I can get for MP3 is 156Kbps) - All tracks play fine with no issues and no pops between tracks.
I have also re-ripped a downloaded 24/48 FLAC file to 16bit WAV - Tracks play fine with no pops between...although It has thrown the track order out of order.
So from this I think I can assume that its dbPoweramp that is doing something to the tracks when converting them??