Hear are some quick fixes for your troubles. You can run these before you play and them re-enable them.
To disable these keys save the following text to a file with the file names listed above the ---cut--- line
(Sorry for the line breaks, don't know why it does that. Each entry should be on one line.)
disable_left_windows_keys.reg
-----cut---
Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Keyboard Layout]
"Scancode Map"=hex:00,00,00,00,00,00,00,00,02,00,00,00,00,00,5B,E0,00,00,00,00
------cut-------
disable_right_windows_key.reg
------cut------
Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Keyboard Layout]
"Scancode Map"=hex:00,00,00,00,00,00,00,00,02,00,00,00,00,00,5C,E0,00,00,00,00
----cut----
disable_both_windows_keys.reg
---cut---
Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Keyboard Layout]
"Scancode Map"=hex:00,00,00,00,00,00,00,00,03,00,00,00,00,00,5B,E0,00,00,5C,E0,00,00,00,00
---cut---
remove_scancode_mappings.reg (restores your default setup)
----cut----
Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Keyboard Layout]
"Scancode Map"=-
----cut----
Hope this is usefull.