What speaker setup do you have?  You've only mentioned L/R/C speakers.  Is there any pattern as to a specific format in the source such as Dolby Digital 5.1, Dolby Digital 2.0, Dolby Digital Plus, Dolby TrueHD, DTS, DTS-MA?  Are you applying sound modes?  This happens with direct/pure direct as well as when having the avr decode something?