first off: If you switch at zero voltage (without the capacitors) and still get losses then your loss specifications are probably wrong or incomplete. Please inspect the loss tables and keep in mind that PLECS uses extrapolation (and interpolation) of voltage, current and temperature to determine the losses at a given operating point. If you want to make sure that losses are zero at zero voltage, add a voltage value of 0 V and set all loss values to 0.
If you feel you still have to use the capacitors (which I wouldn't recommend) you are still free to specify how the losses should be calculated. Since the release of PLECS 3.7 you are not limited to voltage, current and temperature as inputs to loss tables anymore but you can specify custom formulas, custom tables, variables and even use custom input signals for loss calculation. If, for example, you create an input signal that is 0 when doing ZVS and 1 otherwise you could simply multiply the result from the lookup table with the value of the input signal, resulting in the ZVS losses being ignored. Please see the section "Adding custom variables" and "Specifying custom variable values" in chapter "Thermal modeling" of the PLECS manual for more details.