Alistair I'm sorry we didn't mention DAW. We've used Cubase, Nuendo for mixing, while tracking was done on Protools HD3 through a MCI desk. I'm not sure what you mean by "someone coming up with this story" as there's nothing to be gained by making something up here. We didn't think it's the software's fault as the same Cubase session at another studio (actually they ran Nuendo but the session is the same) with PCI desktop setup and Lynx Aurora didn't experience these mixdown problems. The problems only arise when using firewire or USB interfaces with our laptops. We've tried two laptops, both windows XP. FYI we have contacted Steinberg and they said it's definitely not the software.
And The Emu card does have the same AKM converters as Protools HD. Of course that doesn't mean it sounds the same as we all know there are other factors involved in sound quality. In my opinion neither the EMU nor Protools HD3 sound particularly great, everything sounds inherently "modern" through them. Especially after hearing the Prism converters at mastering.
Subvert Beats - Thanks for the offer. The problem is not session specific, it even happens with mono WAVs. Would be happy to send you files although like I said we did a mixdown at another studio (Strongroom) with a desktop setup and there were no problems. If you're by any chance in London perhaps I can get in touch?