1.3.5 using......something weird is going on here.

Once I upgraded to 1.3.5 from 1.3.0.2 it seems like my overrides aren't working and it seems to be using things from the classic template...

Example:
I tried modifying my "Shipping" page and nothing would update when viewed, so I deleted the files (the Define_suchandsuch and yes I had BACKUPS) from my override and the other files (the ones just sitting in hmtl includes folder) and the page still showed up when viewed, but it's messed up, thus the reason for trying to edit it in the first place.

Also is my New/All Product Listing pages supposed to be done in tables? I don't seem to remember this in my previous version...