So this has been going on a while and it's annoying... at some point I was messing with registry or other settings and ended up killing direct download links. I have to copy the link address and add it through Tixati manually in order to download something.

Not a huge inconvenience, but is still odd and time consuming. I've tried uninstalling and reinstalling Tixati, but no change. The system still reads magnet links as Tixati default and if I download the magnet and then click on it, I get Tixati to auto-load, but otherwise clicking all day long does nothing.

Any ideas on what might be going on or how to possibly fix it?

It is a browser issue. Try reinstalling your browser. Use windows restore and set the computer to a date before you messed with the reg.
This last one will work no matter what. Tixati/settings/transfers/meta-info. In the top space setup a directory to download .torrents. In the second space you can then setup the same directory to auto delete after load.
 So now instead of using the choice open in your browser save the  file to that directory.

What browser do you use?