This is happening on my system too, with all three latest releases (1.25.0.9, 1.25.0.10, 1.25.0.11). I haven't used any earlier Snowglobe based viewers.
The problem occurs when I change my UI size and click apply or ok. It also occurs when i make certain changes in the graphics hardware settings. It does not happen with the vanilla Snowglobe viewer.
I've also noticed that my avatar clothing, eyes and skin go transparent if i edit my appearance after the transparent UI background problem occurs. Upon hitting OK in the appearance editor, my clothing is instantly invisible, then a few seconds later my skin and eyes become invisible. No actual change in appearance is needed, just going into the appearance editor and clicking OK will do it. If I then bring up the appearance editor again, all the images are displayed as gray boxes. I haven't noticed any other graphic elements changing. Attachments are unaffected. I become invisible to avatars around me as well.
The background that becomes transparent is apparently also used for hiding the screen when teleporting, the progress bar appears in a window, but the rest of the screen is not blacked out.
I've tried changing various settings to see if any of them affect the behavior after restarting the viewer, none have made any difference. I've changed the stack minimized floaters, hiding the teleport progress screen, Anisotropic Filtering, Antialiasing, Enable OpenGL Vertex Buffer Objects and Texture Memory, Restrained Love.
Changing the following settings invokes the bug consistently:
General tab: UI Size
Graphics tab/Hardware Options: Anisotropic Filtering
Graphics tab/Hardware Options: Antialiasing
(changing Enable OpenGL Vertex Buffer Objects and Texture Memory don't invoke the bug, nor do any changes to the other values on the Graphics tab.)
The avatar became transparent about the same time the following lines were generated in SecondLife.log:
2010-10-23T02:36:45Z INFO: LLError::NoClassInfo::uploadComplete: LLSendTexLayerResponder::result from capabilities: complete
2010-10-23T02:36:45Z INFO: LLError::NoClassInfo::onTextureUploadComplete: Baked texture upload took 6754 ms
2010-10-23T02:36:45Z INFO: LLError::NoClassInfo::setNewBakedTexture: New baked texture: hair-baked UUID: a319ca94-c7c4-1251-bbde-e29f4db64ee1
2010-10-23T02:36:46Z INFO: LLError::NoClassInfo::uploadComplete: LLSendTexLayerResponder::result from capabilities: complete
2010-10-23T02:36:46Z INFO: LLError::NoClassInfo::onTextureUploadComplete: Baked texture upload took 7810 ms
2010-10-23T02:36:46Z INFO: LLError::NoClassInfo::setNewBakedTexture: New baked texture: head-baked UUID: ac1fe9d5-4e62-43f0-e87a-a7348f5e9ecf
Note: Both of those textures referenced by UUID are transparent, as were the other baked textures.
If there's anything else you'd like me to try, let me know. I've spoken to one other Linux user (32 bit Ubuntu) who is also having this problem, including the turning invisible. I don't have the full info on her system, sorry. If you need the full log, I can send it, but there's nothing odd in it when the background goes clear.
My system: