Your cut speeds are wonky. Change them to 2,1 and use that as a baseline for all 3 toolpaths. .4 and .3 IPS is just too slow for that part. It wants to go your target 2 or 1 IPS, but the Z is holding it back. Set it to 2,1 and it should eliminate the problem.
Go read towards the end of this article (or the whole thing if you are bored...) about speeds that the machine likes for 3D cutting: http://www.shopbotblog.com/2008/03/a...m-performance/
Although you can use a ball end mill for both roughing and profile cutting - it isn't ideal. You want to use a square end mill for these. It will cut faster as well, so you can put your roughing stepover value at 40% and leave it. 5% for the finishing pass is too low. You're way into diminishing return below 7-8%. Use 10% as a baseline. By profile cutting with a ball, you'll have a tool radius on the bottom edge...unless you go 1/2 the diameter deeper than the thickness of the part.
I think adjusting your speeds will help or fix the issue...and the settings I mentioned should get you cutting quality at faster speeds. I am not sure why your tabs would be getting cut through - but I do know that if you don't have a setting correct in PW3D, this is possible. Re-check that you have "preserve tabs" checked and "material to leave" @ zero on the cutout toolpath.
Hope that helps. Let us know how you make out.
-B