[weberr]

You can get runnout in a lathe. First, most brand new made in china lathe chucks have a TIR (Total Indicator Readout) of .005", or just over the thickness of a sheet of paper. Compounded with long shafts, chucks that have been abused, chucks that have had a wreck with, bent jaws, etc. that TIR can grow to over .010"

You can easily indicate your shaft and adjust it to run true; You can tap the shaft on the side that is high, or you can use think material such as aluminum foil, paper, plastic to put under the jaw near the high side of the shaft (indicator), etc. Personally, I would check the chuck to make sure it is running true first, as it may be dirt, a burr, etc. on the chuck mounting surface that making the chuck run out.

Personally, I do like to "grind in" the bearing journal on the hex shafts using a whirly jig with a C5 Collet on a surface grinder. But then again, I am the son of a gage maker.

You might be having the gears tooooo close together. I have found that the HEX broached holes and the shafts do have some slop; infact we have tried many different suppliers of the hex stock until we found one that was tight, but not tooo tight.

Good Luck!