So I had a dual boot, on separate drives, for Ubuntu 14.04 LTS and Windows 7 Pro (all 64bit). My Windows install had come first, and then Ubuntu. This was a year or so ago. The other day I felt it was time to reinstall Windows as it was a cluttered mess. That went smoothly. Upon rebooting however my grub menu was gone.
I thought "no biggie, boot-repair will fix it like always" however (all OSes are accessible when I bring up the boot menu with FF11) it reports it was successful but actually isn't. No grub and this is with recommended settings. So I went into Advance settings and clicked "Backup and Rename Windows EFI Files".
This worked in a way I didn't not expect. First it brought me the grub menu, good and all, but the entries were really odd. Ubuntu's entry worked flawlessly but none of the Windows' entries did. Whenever they would boot into Windows it would take two minutes (never had this happen before) and then all my USB ports would stop working as soon as the log in screen appeared. Nothing I do seems to fix it.
So the only way to get into Windows with USB ports working is to press F11 at boot, select "Windows P1 Manager" (there are several entries even in here) from the boot menu (not the grub menu!). This would boot in about 20-30 seconds and give me USB port control again. However it means no grub and no Ubuntu unless I press F11 each time and load Ubuntu that way.
I have no idea what to do. I have never encountered this problem before. I sure would appreciate any and all help!