Interesting problem. I tried a replicate the problem you are seeing with not much success. Originally posted in cdnusers.org by mcatramb91
I have some suggestions / comments:
Is the any properties attached to the Via, like NO_SHAPE_CONNECT, which will cause the via not to connect to the plane?
Is this happening on all Pins and Vias in the design or just a particular Via padstack, Pin Padstack, Plane Layer, etc.?
Maybe there is something wrong with the Flash Symbol PAD_42_FLASH that you are using, have you tried to recreate it?