Submit this bug report to Microsoft. We have very very little to do, really.

Almost a half a year later, still no progress on this really annoying issue.
Server 2008 x64, all updates. Fresh install of both.
I can't fully agree with dmitri. It appears the program uses some nonstandard components and/or messages, because this is the only program with such behavior amongst tens others I have installed after, and amongs hundreds of others I used last years.
Not to mention its interface is not Vista-style, (tabs, scrollbars, menus etc.). Probably this has smthng to do with the bug.
Great software but this bug is ridiculous.

Submit this bug report to Microsoft. We have very very little to do, really.
This is WM_SIZE message that does not go to the components nested at some certain level (depends on the OS) and it's _PURE_ Microsoft bug.

Yes, it looks like a Windows bug (under any OS, even 32-bit versions).Windows stops sending WM_SIZE message if there is too many nested child windows and one of them is trying to resize itself while it's parent still processes WM_SIZE message. One workaround is to use some kind of delay mechanizm and resize child windows only when parent is not processing WM_SIZE message anymore.

It's what we implemented and it works for 99% cases. Unfortunately, it is absolutely not possible to understand what triggers Windows when it stops sending WM_SIZE. Sometimes it breaks much sooner when it's supposed to send WM_POSCHANGING, sometimes it eats WM_POSCHANGED. Sometimes it triggers when nesting level is just 3-4 or even less.

I also am experiencing this issue on both XP Pro x64 and Vista Ultimate x64, so I wrote up a simple helper app that registers a system-wide hotkey. When the hotkey is activated, it sends the WM_SIZE message to all of the PHPEd child windows. I simply have this program set to run when Windows starts, so the hotkey is always available. Works great on Vista x64 with PHPEd 5.2, but I haven't tested it anywhere else so your mileage may vary. The program does not create a visible window, so you will only be able to see it running in Task Manager. The hotkey combination is Windows+Z, so it requires that your keyboard have the Windows key. I've provided the source code so you can compile your own version and modify the hotkey if you like.

- C source code
- The application (compiled with Visual C++ Express 2008)

Hope this helps someone else out