So, I was just doing a mastering of a tune for a friend, and noticed that when your plugins were displayed on screen, they weren't appearing on the tiny little virtual desktop display on the lower right hand of the bottom status bar. The plugs I was using at the time were the PEQ and the MBC2.
Which version of Ubuntu are you using? Just tried it here with 10.04LTS and they show up as expected. The virtual desktop display is a function of the desktop Window manager, so there shouldn't need to be any specific interaction between the application(s) windows and the OS in order for it to 'just work' - however recent Ubuntu versions haven't been as reliable as previously so there could be a subtle bug which has crept in. It shouldn't affect normal use of the plugin UI though.
It shouldn't make any difference, but are you using any unusual desktop configuration e.g. multiple monitors, or any desktop effects such as Compiz etc?