Partially Bored Cylinder w/top grooves

[packinnova]

Hi all,
I'm a complete novice at this design work but the general idea of what I'm trying to do is this:

I have a 5" cylinder.
Starting at .25" down from the top I have marked off a 1" long groove at .5" deep.
Starting from the bottom, it is bored out to a depth of approx 3.5" which makes the sidewalls of that bottom hollow section around .25".

Here's my problem. The machineshop software Won't allow the top groove to dig deeper than the bottom end sidewalls, even though the bored out section ends a good .5" below the grooved section up top.

I've tried to attach the image from emachineshop to see if you guys can point out what I must obviously be doing incorrectly. I suspect you'll get a better idea from the front view...

[Tech2]

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