I've found the cause of my phone issue. It only took/caused 4 or 5 reformats before I got it to where my phone was working properly.
If you go into the phone settings and change the voicemail to put in the password when dialing (2221113333,123456, for example), it causes the phone to stop recognizing further in-call inputs, both in voicemail, and in any other calls where there's a phone menu to navigate.
No deleting voicemail, no pressing 1 to select English, etc.
There are 2 things I envy the iPhone on. Backing the phone up, and voicemail on the phone itself. Is there a comparable way to back this thing up? I've tried doing restores from Titanium long long ago, but it didn't link the apps to the market. I'd like it to save Apex settings, and all the other stuff I spent so long making just right. I really do not look forward to having to spend a couple hours downloading and configuring everything if I decide in the future to see if it's fixed. The only way to return functionality is a factory reset.