Do you know what cam it is exactly? The stock tune will only tolerate so much duration / overlap before it starts to get confused.
I'm not surprised to hear that. I had originally set up the fuel sync in my 5.9 using the method described in that youtube video. More recently I set the sync using the TSB volt meter method and to be honest it seems to run the same, but my fuel economy is way better. Before I changed the sync my average fuel economy was 18.2 mpg, but it started dropping down to about 17 mpg. (I'm pretty obsessive about measuring fuel economy - not because I'm worried about the gas, but because it can help me find issues like this.) I think it was dropping because my distributor cap was getting worn out - the contacts were getting burnt on the leading edge of where the rotor comes around.
After setting the sync with a volt meter I'm now getting 19.7 mpg after 170 miles of driving - with that same worn out distributor cap (I'll change it soon). That 170 miles was a lot of highway driving so I have to drive a bit more to see where it averages out, but I think it will be better than the 18.2 mpg I was getting before.