It looks like you have a filled zone connected, to which those vias need to be connected. Is this right?
Do you want those vias to be electrically connected to the filled zone?
Perhaps it has to do with this fact. For some reason it could be first doing the filled zone shape right, and then, the heat insulation is lost while printing the fab files. Maybe compare the clearance property of that filled zone with the clearance property in the design rules.
Alternatively you could see what happens when you export the gerber files if that filled zone doesn't exist.
Did I interpret your problem right?
--later addition--
As a side note, I have had files seem wrong at the manufacturer's website gerber viewer, and gotten the production fine. This was related to holes positioning though. Of course that I wrote to them before sending to manufacture to check whether the bad visualization was a problem or not