It took a few days but I finally got an answer; apprently when you change the render targets the driver recompiles ALL the shaders which you have loaded. Apprently this problem has been known about since the 10/2006 and that, on XP x64 at least, they have no plans to fix it.
This is poor to be honest, I'm going to confirm it myself, but if it is indeed the case then when I can afford it I'll be jumpping ship to NV. Sure, their drivers might be a mess atm and the R600 might well be faster, but this is a pretty fundamental problem and it renders (fear the pun!) MRT useless on at least one windows platform and possibly more (atm OGL is too flakey on Vista for me to test it); I can wait for the drivers to sort themselves out and, frankly, speed means nothing if I can't do MRT.
Ah well, off to craft an email; I'll report back with anything I find.