I haven't updated windowmaker or needed to fiddle with the preferences for a good while: I think I last set prefs in about 0.53 and I upgraded o 0.60 or so. I remember that such things as running without a dock or a clip needed a restart of wmaker to take effect, but I'm sure this lot didn't: altering mouse focus - from to focus-follows-mouse altering icon size - from default to 24 or 36. I think there were some more. The only thing I could change without a restart of windowmaker was what windows being moved looked like (changed from opaque to boxed) and where the size of a resized window is displayed. These cannot be set without a restart of wmaker , whether you use WPrefs or wmakerconf. Is this what should be happening?
No, I don't think so.
This is an archetectural issue with WindowMaker, and really way outside the scope of our responsibility over this package. It is not a result of any posible compile options, and would require a significant rewrite of Window Maker's configuration system, and run loop. If you really, really need this functionality changed in Window Maker, contact the project at windowmaker.org. This said, I am remarking this as an enhancement, and resolving it as 'Wont Fix'. Sorry :(