My understanding of this is that you are moving the head down in small increments Paul.
I don't have an X3 but do own two 'knee' mills. So if we assume that your mill's head is moving down in a truly vertical plane to the table (and you might want to check it) then another possibility is that the 'tilt' of the head is not set exactly at 90 degrees. Depending which way it's tilted, you will not cut at a true right angle and as you may not have side clearance (if it's tilted the other way you would be cutting a series of ridges) you may also start to deflect an extended cutter no matter how sharp it starts off.
So I'd check both the vertical movement of the head and that the tilt is set correctly as a start.
Another thought – and this is just a personal thing. I don't have the ability to sharpen my end mills at the moment, so I tend to save them for when I really don't have other choices (e.g. narrow slotting). For this kind of job (which I can do easily in a shaper by the way) if I was 'down' cutting on my smaller mill – as there is lots of room on the outside of the work, I'd probably use a 'side' version of a small fly-cutter. Just bar stock with a cutter held at 90 degrees by a grub screw. Very easy to make. Then I get the advantage of an easily sharpened single point tool, no clearance problems and a far less flexible tool holder.
Also, I don't know what kind of lathe you have but with a large enough chuck, a sharp tool and very gentle cuts I think you could face off this bar in your lathe. The cut will be interrupted on the corners but will be fine once into the centre. You will probably be able to see the cut 'transition' but it should still be flat (given that "flat" is a relative term!).
Anyway – hope this gives you some other things to think about.
Regards,
IanT
Edited By IanT on 20/10/2014 10:45:49