7D focus better without IS?

I'm still exploring my 7D and am more than ever convinced I made the right choice upgrading from the 50D.

I've spotted one oddity, which I suspect may point to a fault with my canon 300 f4L IS, so hope others may be able to comment on it.

Using this combination with static objects, IS on, the images were razor sharp from MFD to 50 ft ish

When I dialled in +5 MFA they were sharp with IS up to several hundreds of feet (I use a standard focus object which is a sand sorting tower on a distant water works and the results were significantly sharper than anything I got from the 50D + 300 F4)

It was when shooting birds in flight that I started seeing inconsistent results, whether I used mode 1 or mode 2 stabilisation

So, I switched off the IS and, bingo, consistently sharp images of gulls, pigeons and magpies in flight (same with small aircraft as well)

So, Static images, IS on, sharp at all distances

Small, moving objects - inconsistently sharp (mostly blurred) with IS

Small, moving objects - consistently sharp with no IS

I know that the IS on the 300 F4L is an old design (and is certainly not up to par with my 70-200 F4L IS, which doesn't show this effect)

If you have got this far - thanks, my query is: are others seeing the same effect with their 300 F4L IS or is mine needing an overhaul?