No DVI mode does not make a difference.
I also keep getting inconsistent refresh rates with the SNES with the same game. Sometimes its 15.73khz 60.05hz. I turned it off over night and tried it this morning and got 15.74khz 60.08hz. It will work fine in 2x mode, but when I change it to any other mode, the video goes out. I can get up to 5x mode through the capture card for the N64, but its just so blurry.
When I chain it to my XRGB2-Plus (which seems to be the only solution right now), I get 31.46khz 60.05hz.
I have also tried switching out Scart cables from the CSYNC cable to the Luma Scart with no luck.