What I'm seeing: If there are voids in the x-ray and you have noticed solder in the vias on the opposite side, then the solder is flowing on the PCB pad.  If the component pad isn't wetting, either the pad isn't solderable or there isn't enought solder due to inadequate paste, poor reflow, or vias sucking the pad dry.  If paste volume on the thermal pad was reduced by step down, the paste on the leads might be keeping the thermal pad from contacting the paste (extreme case).

I try to place vias in a pattern that allows them to fall between (not on) the panes of paste, forcing the solder to flow a bit before getting to the vias.  Not a cure-all, just trying to help.  Filled vias are the safest way to keep solder out of vias, but add cost.  Capping vias with soldermask brings it's own set of problems, but if you must I like the mask color to be Blue - no - Yelllllllll

Pete