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Perfect delay-free NES emulation and delay on HD-TVs


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I've been on a quest to achieve perfect delay-free NES emulation and I was wondering about the experiences of others.

The two main emulators I use currently are Nestopia and VirtuaNES. I find VirtuaNES to be better on the delay side with its VSync method, which is apparently implemented differently than Nestopia. With all the video processing on (scanlines etc) and in full screen mode, I can get tear-free 60fps at near-zero lag. It's great. How has everyone else's experience been?

So, on to my main question: I've been trying to output from my computer to my HDTV on HDMI and have been having a strange and frustrating problem: For some reason, this introduces delay! After much time spent tweaking my emu settings to get everything perfect, it's rather frustrating.
I've read all about this problem. Apparently HDTVs have delay when they are required to scale video feeds from "weird" resolutions to their native resolutions. The other common reason for lag is due to video processing (Motionflow on Sony TVs, etc).

Now, I've shut off all the Motionflow and processing stuff and made sure to put the TV in game mode and there's still a small delay. Here's the thing: When I'm on my Windows desktop there is no lag! There's no lag in the mouse movement, and if I play a game in VirtuaNES/NESTopia in a Window, everything is perfect. However, when I put the emulator to full screen, lag appears! I am making sure that the emulator's full-screen mode is a native resolution of the TV too (1080p).

Does anyone have any idea what could be going on?? Why would the same 1080p resolution settings on my standard desktop not cause any lag, and yet the emulator does? Are the color settings relevant?

Has anyone else had this issue? How did you solve it?