Final mission problem

[Torchfire]

So far I experienced the following twice: When fighting in the final mission (according to the walkthrough, it's the one with the giant turtle-squid thing), I get EMP-d, which is understandable, but after the EMP shield recharges, controls don't return, leaving me dead in the water with no way of completing the mission. And from the amount of hits that I take, geting EMP-d is inevitable... The game still runs, though, and ESC still brings up the menu...
I got EMP-d in earlier missions and controls always returned after the shield recharged...

Is there any way to avoid this? Or fix it?

Update: This only seems to happen when using the Phobocaster. When I swiched to the Voodoo Breath, it restarded normaly after an EMP. But it maneuvers like a floating brick, so the mission is much harder with this boat...

[Titan Arum]

I have the same, only with the Phoboscaster...