I'm still getting the input lag when running in fullscreen.

PC Specs:
Windows 7 x64
3.0GHz Intel Core2Duo
4GB RAM
nVidia GeForce 9800GT
Monitor 1:1920x1080 [This it the one I am running NESTopia on]
Monitor 2:1440x900

NESTopia Settings:
Video:
Device: NVIDIA GeForce 9800GT
Mode: 1024x768
Filter: Standart [No Scanlines, no Bilinear]
16 bit
Memory Pool: Video
Monitor Frequency: Auto

Timing:
Synchronize to Refresh Rate
VSync
Use high-precision timer
Enable triple buffering
Default speed

I think that's comprehensive enough. If not let me know and I'll post the log/xml.