Well, LBC and Firefox (v 3.0.5) don't play very nicely together. LBC is set to stay on top, autohidden, and with everything else I've run so far, the thin line is visible to the left of the screen and I can access it. With Firefox maximized, I can't - some of the time - but, usually, all I need to do is minimise it. Then I can get at LBC from the Desktop or whatever other program happens to be on top. I haven't noticed any other programs "blocking" the On Top feature so far. Just a guess, but since it is an 'on and off' sort of glitch, I wonder if that part has to do with some sort of code in the web pages I visit, or something similar. I'll have to try to notice what pages initiate the problem, if there is any correlation there.
The other part, the one I posted about, has happened several times - always after the screen has powered off and been brought "back to life". Then, I can't find LBC at all, no matter what windows I minimise, and moving the mouse to the left side of the screen won't make it appear. Since it seems to correlate with the screen power / display in some way, I suspect that is just my system being ornery. I was mostly hoping someone else had noticed a problem on their own system and figured out a workaround.
Since it is a desktop and not running on battery power, I suppose I could just change the power saving settings to keep the screen from shutting down - I'm holding off on that so I can observe and troubleshoot at the moment. But if anyone does know what's happening and has an idea for a fix, that would be cool.
Just in case any of those minutiae gives you a clue to the issues I gather you're having with the On Top feature.
(Which usually seems to work fine for me, btw.)