I do use A TC-50M as a controller.
ok had a look to the Manual, in this case i think 0 for step/dir pules is ok/does not matter.
back to the Basic Problem.
did you check the real distances as described (MDI G1Xsomething) and measure ?
same for Y axis.
anyway, if the real distances match to to the DRO's, X and Y should move the same Speed.
you can also do a simple test via MDI
G1X300Y300
should give a simulitanious move of both axis.
by rereading all the post's i recogiced that your machine is belt driven (my bad english,and the Age).
ok that means one motorrevolution is 40mm, right?
in this case your motortuning of velocity 400mm/min is very low (what actually means for the Motor 10 rev/Min).
don't realy know what Speed you expected to run?, but i think for a woodmill (have no Experience with Wood),
it is IMHO to slow.