Oh... alright, I guess then there's no way around this. Skype unfortunately has no option to tell it to not do this, and I can't just change the default behaviour of my keybinding used for closing windows to specially be changed for skype. Though, not a bug related to PekWM anymore.
Thanks. Set the status as invalid.
I assume that the skype window is not hidden but actually closed. The program can run in the background without having a window open (or iconified for that matter). Perhaps you can disable this in skype's configuration? Or you might try to use the 'kill' action instead.