I don't know if this is relevant or not, but...
I am running Actual Window Manager with a taskbar on my second monitor showing only those applications running on the second monitor. I have noticed since turning on persistent taskbar that when I switch away from the desktop with Eclipse on it, Eclipse will sometimes (I haven't found a pattern yet) move to the primary taskbar even though it's running on the second monitor. When I switch back to the desktop that Eclipse is actually on then it moves back to the correct taskbar.
This may just be a bug in Actual Window Manager, but since Eclipse is the application that disappears most often for me, it seems like more than a coincidence that it's behaving oddly with regards to taskbars, too.
More on disappearing Eclipse windows: if I have two Eclipse windows open, switch away from the desktop with them on it, and switch back after a few minutes then I'm more likely to lose one of the Eclipse windows--usually the first one I opened. I haven't yet observed this with persistent taskbar, but it did occur with persistent taskbar disabled frequently in the past.
Edit: I just experienced the same behavior with IBM Lotus Notes. It seems there must be a connection.
One other potentially useful bit of information: my primary monitor is excluded from desktop switching. Are these applications somehow getting moved to that monitor temporarily when I switch away from the desktop they're on?