I've been slacking off on my reading and reporting on any problems.
Should've first posted this back in July.

After reading sclg's post about Skype v4 I must say I have the same
problem but with the PortableApps Menu.
I too did research around the same time and found the ObjectDock
reference in the PortableApps forums.

When the new NS systray code/fix was introduced it broke PAM.
I'll start PAM and it'll work fine like when I'm installing portable apps
into the menu but what happens is once you launch an app the menu
will disappear as normal but when it's brought back mouse clicks no
longer work (during installs PAM stays put otherwise it would be a real
problem). You can move the mouse around and see items like
buttons hilite but clicks do not work.
The menu has to be exited via its systray icon menu.
PAM is all but useless when NextSTART is handling the systray.
If I want to launch or test portable apps I can no longer do it via PAM
and must use one of my alternatives like PStart.

Apologies for not mentioning this when I first noticed it a few months
back.

There are a couple of other issues such as the menus from my Bluetooth
icon not working at all while NS handling the systray.
I'll have to test that one a bit more. I only recently started using BT to
sync my Pocket PC after a lot of strange things started happening via
cable connection (starting in July also - coincidence I reckon). Including
WorkShelf and all its modules totally freezing up.
Couldn't kill WS to save my life but when I unplugged the Pocket PC WS
disappeared. Only WorkShelf freezes, everything else still worked
(I really dislike ActiveSync).
But that's another issue.

Marc