Super Nintendo direct RGB Capture with DVI2PCIe Card Take 2
I tweaked the sampling rate on the capture card and tried a different resize filter. Managed to get rid of the flagging on capture and came close to pixel perfect results. My pre-1CHIP SNES is likely the cause of most of the noise and slight blurriness.
Original video was captured at 512x240 in 24-bit RGB and resized down to 256x240 (native SNES resolution for most games), then resized back up and padded to 1280x720 using VirtualDub's internal Resize filter. Its Nearest Neighbor resize eliminates the added noise from the SNES output.