Default N7105 - / folder messed up

Hi, so I tried a few roms and reverted back to stock today.

I've flashed CM10. 2, aokp and MIUI.

Now I've restored my stock rom backup wiped everything and boot the phone. Everything working fine. But then I went to es file explorer and find out that the / folder is messed up...

And my internal storage is mounted in a crazy spot... I've read that cm causes the 0 bug because of the profiles. But this is different....

How can I completely format the / folder and flash back the stock rom so everything is back to normal?

Thanks

Sent from my GT-N7105 using xda app-developers app
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My Android history:
Commtiva Z71 (CM7)->Galaxy S2 (CM9)->Bq Edison (stock)->Xperia U (SS v4)->Galaxy Note2 LTE (MIUI V5)

Daily Driver: MIUI V5 3.12.20 by kat0072