First Close Pro Tools

Open C:\ Program Files \Digidesign\ Drivers
Double Click on the EXE file MMERefresh.exe

Note: It will appear that nothing has happened the process is fast and will only be noticable by brief appearance of the hourglass

Now open Pro Tools and check to see if the midi ports are available (check any Midi tracks input)

If the 002 midi ports are still not available you may be required to trash your preferences

To trash your preferences Win XP / Pro Tools v6.1

DAE prefs are located in...
C:\Program Files\Common Files\Digidesign\DAE\DAE Prefs
Put the DAE Prefs folder in the Recycle Bin

Pro Tools Preferences are located in...

C:\Documents and Settings\"your user name folder"\Application Data\Digidesign, trash the Pro Tools LE v 6.x preferences

Note: if you cannot see your Application Data folder it may be hidden you can make this file visible by going to Tools menu > Folder Options > View Tab > select show hidden files and folders and click apply