It probably has to do with file association. What OS are you using Mac/Windows? When you export a file and you choose Adobe PDF (Print) do you still get an HTML? Indesign remembers your last export selection. If you need other format you have to choose it from the list.
So, I ended up uninstalling and reinstalling InDesign and was able fix the file association issue (thank you so much for the heads up about that).
However, whenever I export a PDF (Print) it is still only generating a HTML shortcut to my desktop instead of the actual PDF file.
I'm running Windows 7 Home Premium. However now I feel that the issue is more based within InDesign. I have no idea what I did to make InDesign start exporting my PDF's this way.
So, looks like I figured it out. The file associations is what did it. For some reason it was it was using Firefox to view the PDF. I wondered if it was doing due to some update with Acrobat.
So I reinstalled Acrobat. I saw that when I exported the file the extension changed from .html to .pdf.
So then I right clicked on the icon>properties and it let me change the associated program to Acrobat instead of Firefox.
I'm not sure if that is what needed to happen, but it appears (at least for the moment) that everything is fixed. I'm going to go tomorrow to see if I can get it printed. Hopefully everything will have exported correctly.