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I have an Enco 12x36 lathe and the D1-4 3 jaw chuck that came with it always had a lot of run out. Finally on closer inspection I noticed the backplate did not mate up to the spindle face--about .005 gap.
Don't know if this was the correct way to fix it, but I took the backplate off and chucked it up backwards (taper facing out) in another 3 jaw minus the studs.Then took some 120 grit emory cloth and went to sanding on the taper.
It was a real pain to do. Sand some, reinstall studs, remove chuck, install backplate and check gap. It took me about 8 times of doing this but finally mated to spindle face, Chuck now has about .002 to .003 run out.

As long as the taper lines up reasonably well, it should fit consistently. Or, find the best orientation with the least run out and put some witness marks on the backplate and spindle nose to align the chuck when reinstalling.
I have also turned a standard chuck into an adjustable type chuck - like the Set Thru's by taking 5 thou off the register boss on the front of the backplate. You can crack the mounting bolts loose and tap the chuck around till you have minimal run out on a workpiece. Just make sure the bolts are tight when done so it doesn't move around.