If you can, upload your part so your workflow/settings can be reviewed.
If not, post a screen shot of your hole wizard settings.
EDIT: if you need forum upload assistance, see this post: How can I attach a file to a forum post?
If I'm interpreting this correctly, I don't think there's an SW issue here:
- Drill depth is full diameter depth, not tip depth (this is even shown in the wizard depth image)
- Your listed drill depth value is more than your tap depth.
- Bottom taps don't cut to their end, they just have less lead-in on their first few threads than do "regular" taps (unless you cut off the end of a tap, which I've done, but just to get an emergency bottom tap to add more thread to an existing hole).
- Tap lead-in isn't steep enough to go into the drill tip space.
- Unless you end mill/drill-mill cleanup your hole, taps don't have the strength to remove the material down to the drill tip point.
If you need to show a square bottom threaded hole (even though you won't really get one), then I think you'll have to model it that way.
Add a HW tap and adjust your settings accordingly.
Extrude cut to remove the tip material..
Keep in mind, your callout will reflect your HW settings, not your cut depth.