Xubuntu Jaunty- new fresh install Clipboard Manager does not reliably remain in the panel. It disappears and has to be reinstalled frequently, both between sessions and within a single session. I cannot identify any pattern or settings leading up to this. Not sure of version number- whatever comes with Jaunty 9.04. I had the same issue with earlier versions of Xubuntu. This is the ONLY panel plugin that behaves this way.
Well, the version can be figured with dpkg, and by looking on http://packages.ubuntu.com/<package-name>. It is 0.9.0. The version 0.9.1 was a so-what-called bug fix release, but I doubt it fixes your issues. The 0.9 version is unmaintained and the plugin is already rewritten and released at least under 1.0.2 version. 1.1.0 will follow next. It should be possible to catch a backtrace with gdb, you have to run the plugin in the panel than figure its PID, open a terminal and type ps ax|grep clipman-plugin, and finally run gdb --pid <pid>. In the gdb prompt you will probably have to type continue. Than when the plugin disappears you could be able to type bt, copy/paste the output and quit gdb. The plugin might still be visible when it crashes while being attached to gdb. From a backtrace, we may be able to have a better idea, and perhaps get a fix.
Any news? I'll close this bug soon if there is no activity. As said 0.9.x is unsupported... maybe you can get in touch with the maintainer of the ubuntu package.