My new installed copy of Photoshop CS6 has a few problems:
1. When you go to save as the file formats selctions are not what you get. For instance jpeg gives you EPS. Multi Picture Format gives you jpeg. What gives?
2. One of the plugins that worked fine under filters is missing. When I copied the things from the old CS5 plugins folder to CS6 folder it still is not showing up... What gives?
Your own fault because:
When I copied the things from the old CS5 plugins folder to CS6 folder
You made a mess. Remove those CS5 plug-ins and get the proper CS6 versions from the vendors.
See this FAQ for information on Plug-Ins