Ok, if I set the "Restore Window geometry" for certain windows, it works.
With a clean compile of trunk and empty configuration, are these not filled in by default???
"Restore Window geometry" is selected by default at least for me. I am running Linux now but these settings do not depend on OS or widgetset.
It is very possible that your local configuration is corrupted. All environment options were revamped. Some intermediate versions of trunk have surely been broken.
I suggest you start with a clean configuration. If you run both the release version and trunk, you should use --pcp parameter and different configurations.
For example :
$ cd lazarus_trunk_dir
$ lazarus --pcp=.\lazarus_trunk_cfg
should work on Windows. Or, give the whole path for configuration :
$ lazarus --pcp=C:\lazarus_trunk_dir\lazarus_trunk_cfg
... or something similar.
You can create shortcut icons to your desktop with these parameters, too.
Now I am interested if the transition from Lazarus 1.4.x release to Lazarus trunk breaks the configuration somehow. The desktop feature has stabilized and the configuration should be converted automatically and gracefully.
If it however breaks then please report here or in bug tracker.