That's not what's happening. Auras aren't applied every game update cycle, but only every couple of them. So when pause building if not on the right update cycle your thing won't get the buff but if there's a sniper off cooldown it will see and shoot your thing. Only workable solution right now is to get enemy snipers on cooldown by building a pile of crap at edge of system, and then build the wanted things and delete the decoys.
It's the same problem with gravity turrets sometimes not slowing fast waves until they have reached the turret, in that case the only solution to force applying gravity is to save and reload as auras are applied on load.
edit: and a happy new year!!!!
