It was 2 operating systems on my machine, Windows 7 and Ubuntu Desktop 12.04, both 64bit version. All works well, firstly I installed Win, then the Desktop version of Ubuntu, lasts's GRUB rewrites windows's boot and of course added it as a variant to load. Yesterday I wish to play with Ubuntu Server 12.04, and install it as a third operating system. During the installation Server's GRUB seems to rewrite that which installed earlier (background color became black, was purple). Firstly, newly installed GRUB generates me overmuch load options for Ubuntu Desktop, by two for each kernel version (normal and recovery modes). OK, it's bearable, but most thing, that the mouse on this machine is totally stops responding, regardless which operating system I choose to load. Hope somebody help me. Thanks in advance!
It's next to impossible for Ubuntu Server installation to affect the functioning of the mouse in Windows 7 - no code from Ubuntu is ran when you boot into Windows 7, it's just bits on your hard drive.
Check the cable, maybe put in new batteries if it's a wireless mouse.
I would also try unplugging the mouse after Windows has loaded and plugging it back.