How different are your concentrations? Can it be accounted for in the mass balance of the sample? As the boiling point for aqua regia 2-1-5 is 101 C and conc is 108 C. You may be vaporizing off a substantial amount of aqua regia thus changing your base volume. Also your dissolving of nano particles should be nearly instantaneous at room temperature. This would give you better control over your final volume as the room temp vapor pressure is much lower than at 100C.

Some more trivial advices:

1) The calibration should be in the same acid mixture / acid strength as your samples.

2) To keep gold stable in solution reasonably high acidity is needed. My choice is either aqua regia diluted to 5% or 5% HCl with a tiny bit of nitric acid, but HNO3 with a little of HCl might work as well.