Make sure that no axis are against the limit switches when it powers on.
If it wakes up with a limit switch, it can be REAL grumpy.
Move the axis off the limit or homing.
Also, when in E-stop, press the align key, then F1
Then RESET key
This will clear a possible PFI Power Feed Inhibit state
After that you need to HOLD the green key down to power it up, and continue holding it down to jog any axis off the limits.
And how do you KNOW that all the limit and homing switches are working all the way back to the control?
Did you go into the maintenance screen and see it toggling in the software? I forget the diagnostic screen names to see the actual I/O bits going ones to zeroes.
Any problem all the way back into there can give bad results.
Did you go back into the configuration screens to see the approach speed of the axis?