Win+R -> regedit.exe
HKEY_CURRENT_USER\Software\Team17SoftwareLTD\WormsArmageddon\Options
ForceWineVirtualDesktop=0
or if using WA.ini (PrivateCfg):
ForceWineVirtualDesktop=0
PS. May I ask you, HOW did you manage to enable that on Windows, except modifying registry/ini files.
Also, the repetitive color bug could be related to auto-changing wallpapers (if you use them).