No, this is definately later in the game. The "giant-butt-whooping-wave-before-15-seconds" is definately fixed, but it would appear that after about 1:30 the threat slowly starts rising, and it's almost 95% high mark ships (IIIs and IVs, sometimes the occasional V) and will keep rising as you get attacked by these high level ships. There seems to be no end to it either.
Just as you think you fought them off, another 50 or so come through a wormhole, and since Tractor Turrets cost 36 000 crystal these days, you 0% chance to get any up to catch these waves, which means they completely slaughter your economy, grinding you to a complete stall and then work you down from there.
It's quite frustrating and I've actually stopped playing for now, because I find myself losing temper and become angry, and that's not the way it's supposed to be.
If you need me to test anything specific, please let me know, but I'm not playing casually until this is fixed. Sorry