A couple things to check. Do a JH (jog home) and see what happens from anywhere on the table.
Then start at the same place and do a MH (move home) and see what happens. On mine if i do a JH, if the bit is say 1" above material surface it lowers to 0 above surface and jogs home. If i do MH the bit stays at it's height and moves home. Don't know why, but rather then "fix it if it ain't broke" i just deal with it.
I think you need to check your "start position" like Scott shows in his picture. I think what is happening is your bit is "topping out" and you just don't see it or hear it.
Leave your router/spindle off, Take a small scrap the same height as your material. Zzero to that. Move the scrap piece away. listen to see if you are topping out. Run the file and check your bit heights.
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