It was shot at 1/160s with rear shutter curtain synch. The rear drop shadow is the movement of the flying fox before the flash kicked in. But that's the sort of problems I'm trying to work around. If I shoot at faster speeds, I can avoid this, but then I lose detail in the sky and if I shoot faster that 1/250s then I'm also stuck with HSS, and the bats are too far away for this to work effectively with the gear that I have. To counter that, I can increase ISO and decrease flash power, but increasing ISO results in more noise. Its hard to get the balance right.
Hmm. I guess that's a plausible explanation. Based on the actual offset of the shadow, it was moving at a vector of about 120° then...as the shadow is not directly behind, it's offset to a about a -35° angle. That seems a little odd...but, eh.
I think you could crank the ISO up more. The 1Ds II isn't that bad...it's certainly better than the 7D, despite being older, and the 7D is pretty good up to ISO 800. Also, that is indeed how clear and sharp the bats are after the flash, then that means they are easy to mask. With masking, you could clean the background noise right up! You might even want to look into PixInsight, which has some of the most advanced multi-scale noise reduction tools around, but Photoshop or LR could certainly do it as well, I mean you could completely obliterate the noise once you have the bat masked. If that's the real problem, and that shadow really is caused by flash lag with rear-curtain, then I think you could crank ISO by at least a stop, if not two, and use two stops faster shutter speed.