If you double-click on the I/O Units folder, you'll get a list of all your I/O Units, with columns for the Name, Type... and Ref Count. Does your Ref Count show a non-zero number? If so, it's possible that Ref Count got messed up. Close the window, do a Ctrl+R (you may see a "Generating Reference Counts" message box pop up momentarily). Then go back in and see if it's zero (in which case you should be able to delete it).
Also from your strategy tree, try doing a Right-Click on the I/O Unit in question, then Find... to see if/where your strategy things that I/O Unit is referenced.
If you're still having trouble, do File > Achieve strategy and send the .zip file to support @ opto22.com since they might be able to get it sorted out for you.
Hope that helps!