I have the same behaviour using Anjuta 2.4.1 under Ubuntu 8.04 (Hardy Heron) but it affects all glade plugin panes, also including widgets and palette.
Also the positions are forgotten if I close the glade document, even if I keep the Anjuta session open.

Probably glade plugin should be user-activated, so the panes will not disappear after closing all glade documents.
All positions are saved normally after restarting anjuta for me and you shouldn't try to reopen the session in any other way because that part of glade plugin is broken (at least for the current version of glade plugin). My working version doesn't have this problem but it still forgets positions when deactivated.

Okay, as part of a session, Anjuta only remembers what was there *just* before it was exited. If a plugin goes away before anjuta exits, it doesn't know about it. It's just a design issue and there is no straight forward way to fix it. For example, consider this example (keep aside the fact that anjuta currently does not have per plugin layout saving for the time being):

1. At this point in time, you have an uber cool layout.
2. You close the glade file/plugin and anjuta remembers glade widgets.
3. Two months later, you are now in another uber cool layout -- a very different from what you had 2 months ago.
4. You open a glade file.
5. You current layout is so different, Anjuta doesn't know how to restore/map the previously saved layout for glade plugin -- that's the problem.

Anjuta doesn't even know if the saved layout information is even compatible with your current layout (so that it could consciously discard the saved layout and use defaults).

This is a non-trivial problem to solve and would require good dose of computer science. Anyone is welcome for the challenge :). Just a little bit of information. The layout is stored in a tree structure (means for the same visually looking layouts, you could have multiple tree structures). We could try to come up with some heuristic algorithm to merge them that relies on structure's 'visual impact' and some magic. But I have other things to do ;).

Thanks for the bug report. This particular bug has already been reported into our bug tracking system, but please feel free to report any further bugs you find.

*** This bug has been marked as a duplicate of bug 569160 ***