A control system comprises a cam position calculation module that determines intake and exhaust cam positions during operation of an engine. The engine includes a regeneration and fuel cut-off (FCO) mode. A cam position adjustment module generates alternate intake and exhaust cam positions during the regeneration and FCO mode. A cam positioning module positions the intake and exhaust cams based on lower values of the intake and exhaust cam positions and the alternate intake and exhaust cam positions, respectively, during the regeneration and FCO mode.