A while back I had the same trouble.
I noticed that hole wizard had remembered some uncommon numbers for far side countersink & near side countersink. (Even if they are not ticked)
I had to tick the checkboxes (near & far side countersink) and set their values to zero each time.
Later I found out that my hole wizard favorite was corrupted. I deleted the favorite and create it once again.
and everything was OK again.
I know I saw this happen on my system a couple months ago and a co-worker and i looked at it, looking at details I know we saw something that looked weird, selected something else or de-selected something and it went a way and never returned -
Unfortunately, I don't remember what that was.
I was trying to search the forum a few minutes ago but didn't find anything.
Maybe I had the same thing you did - but I don't think I had to delete anything.
The only workaround that I've found that seems to reliably work without needing to resort to drastic measures of clearing the registry or some such thing is to find an existing hole of any size or type and copy/paste it into the part you're working on. Then edit the feature to have the thread you actually want it to have. I'm assuming that this would also work with other hole types as well.
Admittedly, this is a fairly redneck workaround, but it's the only solution I've found that actually works.