In Super Mario Bros 64 1.2 when running in docking station mode in NTSC, the sprites all seem to be shifted about 8-10 pixels to the right of where they should be in relation to the background. This is very noticeable when hitting bricks from underneath. If the character is a little to the left-of-centre of the brick, he passes through it. If you connect, the brick immediately shifts to the right before animating. Walking into a pipe from the left results in the character embedding himself into the pipe before stopping, approaching from the right results in him being stopped before he even touches the pipe.
This doesn't happen in PAL mode, or if it's connected to an NTSC C64C in cartridge mode, so it seems to be an issue with the FPGA implementation of the NTSC VIC-II.
Also, colours from the VGA output seem much more washed-out and dull in NTSC mode, while they look rich and vibrant with it set to PAL. The default yellow colour in the TC menu is particularly bad for this. It's almost white in most NTSC configurations. On my 1702 monitor from the same C64, the NTSC colours via composite are as rich and vibrant as the PAL VGA output in the TC64. This was reproducible on 4 different LCDs (3xSamsung and 1xNEC)
I'm running the VGA output at 800x600 60Hz when in NTSC, and 800x600 50Hz when set to PAL.
