If this happens because of the known flash problem, there is nothing we can do. Can anyone reproduce this with <=gtk+-2.16?

Strange things happens with Flash in general. For example, buttons in many Flash apps doesn't work, buttons in embedded videos also doesn't respond to clicks. They (interactive objects) react when you hover mouse pointer over them. Work around for Flash apps is to open menu from r-click on such app and then do quick double click on desired button. This works doesn't work with Flash preferences window, though.

Some Arch Linux users suggested that downgrading GTK works (to 2.16?). This would make sense, since it started to happen after upgrade of GTK (way back then), not PekWM. BTW: PekWM 0.1.12 still has this bug.

No, that doesn't change anything...

Does setting GDK_NATIVE_WINDOWS=1 prior to starting firefox change anything?

I also tested this with flashplugin-prerelease 10.1.51.95 now, but the buttons still don't work. I'm running archlinux 32bit version.

pekwm --info says:

 pekwm: version 0.1.11 Built on Fri Jan 22 07:11:39 UTC 2010
 features:  XShape Xinerama Xft image-xpm image-jpeg image-png Xrandr menus harbour

flashplugin version 10.0.45.2.

I tested this with opera, firefox and epiphany (with webkit) and it always occure.

More interesting focus issues here.

Assuming this is within firefox? What version of flash?

This will happen only with pekwm, I tried it with many other wms