So I have done a fresh install of skyrim. no mods installed/ I run boss and it places skyrim.esm in the unrecognized plug ins and lists it twice?? I am confused.

Did you start up Skyrim before using BOSS? Are you using the script extender?

ah I haven't downloaded SKSE yet. Its a fresh install. I also seem to be having a problem with Wyre Bash. Just installed the latest version from Nexus and followed the installers instructions/followed the set up guide at STEP's site. and it just flashes a window but wont start.

PS just installed SKSE and it still doesn't recognize skyrim.esm

I did start up skyrim before launching BOSS. I just played the opening scene a bit. road the cart for 10 seconds made sure I had the right versions etc and quit the game.

Hate to ask this..... it's a legit copy?

yes it is. I fixed it. This is what I did. I deleted my DLClist.txt, Plugins.txt and loadorder. text in c:\users\appdata

Why exactly did that happen? I got the solution from wyre's instructions on nexus but I didn't do what he said causes this error lol.