As Uncle Gizmo said double check your connections but this is a known issue with some virus'. It has probably corrupted some system files (probably keyboard.sys). The best way is to do a system repair as this will catch all files that may have been damaged.
If you have windows XP:
First just check to keyboard is actually working before windows loads by pressing either del or F2 (could be another key depending on your BIOS) when the system first starts (i.e. when you see the simple white text on black background) to go into the BIOS.
If that works then great - whilst in the BIOS navigate to the boot options (this will be in one of the menu but it varies from BIOS to BIOS) and check that the cd/dvd rom is set to boot first before the hard disk.
Save (if required) and reboot with your XP disk in and when you get to the welcome to setup screen and press enter - To setup windows XP now - NOTE not the repair a windows installation.
Follow the 'wizard' until setup has detected your installation of windows, you will then get the option to repair this copy of windows. (Don't setup another installation of windows choose the repair option)
Let windows do it's thing i.e. go for a cup of tea, have a run, wash the car go for a pint etc.

and voila everything should be sorted.
This will repair any damaged system files that may have been corrupted and don't worry it won't do anything to your prog's setting etc. it will return to the way it was before.
If you have any questions post back - good luck