Binary package hint: gnome-panel
This problem may either be in gnome-panel, nautilus, or compiz-fusion. I'm not sure how to upload files, so if someone e-mails me I can provide more information. I have an Intel Mobile 945GM graphics controller, GNOME 2.2, Ubuntu 7.10 beta, and compiz 0.5.3.
When I first log in, the top panel is not visible. It instantly becomes visible as soon as I click on either where the panel is supposed to be, the desktop, or one of the desktop icons. Click on the opposite panel does not make the other visible. When I first installed 7.10 beta, I switched the panels (top to bottom, bottom to top), and I noticed that an "image" of the panels were still there, even though the image was not an actual panel (could not click on anything on it). I moved one of the panels to the left side of the screen, and there was still an image at the top, though the working panel was on the left. Strange. I don't know if this is relevant, but I've been surprised in the past, so I'll mention that my bottom panel (the one that actually shows up on login) was modified to have 50-pixel icons, dynamic sizing (by unchecking "Expand"), and partial transparency. The top panel has standard properties, and only the contents of the panel have been changed (either added or removed items). The main menu is on the bottom panel.
I hope this helps, please contact me if you need more information (which you probably will).
I'm experiencing the same issue, but with the bottom edge panel (show desktop button, workspace, and trash applet) on Gutsy and Gnome 2.20. On login the panel is invisible and I have to click on it or anywhere on desktop to to make it visible. The only modification I did was resize both panels to 21 pixels. Main menu panel is visible on login.