I think the SS's soft limits work a bit differently from the parallel ports soft limits but been a while since I have messed with them. Try setting a larger slow zone in Homing and limits page and see if that helps.
Also you may or may not want the X to raise on Stop, prefer it not to, if you dont want it to do that you can disable on the Safe Z page, I prefer to use machine coords for safe Z and just set that accordingly, that way I know it will always go to a set position, mine is -2mm so it is just 2mm before the axis extent. I however have servos with fast acceleration/decelleration so I can be close, if your acceleration/decelleration is slower you may need to set a larger amount.
Hood