DRC flagged all GND via's with "missing thermal". It was fine as I applied DCR along the way laying out the board, now it's almost done, all of a sudden, this "missing thernal" flag shows up on all my GND via's. Does it have something to do with the ground copper pour being applied?
Yes, it is to do with the copper pour.
Vias do not normally have thermal relief. Thermal relief is applied to a hole when a through hole component is going to be soldered in to it. The thermal relief allows the solder to flow easier, otherwise the copper plane would steal the heat and may make a poor solder joint.
There must be an option to turn off thermal via checking in the DCR set up dialog.