Turning off Ubuntu 8.04 with Xiphos 3.0.1 still on, and starting Unbuntu again, Xiphos shows up for some moments, and then gives the error messages: Xiphos does not understand more than one argument.
There are more than one error message. Their number equals 1 (for the program) and one message for each resource in a seperate window.
I'm getting a similar thing on gOS, which is an Ubuntu-derived operating system. I've discovered a quick solution.
I don't know what the real solution is, but this got me up and running again.
based on the observation about app_y being weird, what i've done is to add some paranoia code that clamps app_x and app_y to reasonable values. i believe xiphos gets an insane reconfig event as the system is shutting down, leading to app_y == 2406. (no real monitor is 2400+ pixels tall.)
i am not sure this will fix the problem as originally reported, but it's at least a very good stab. file a new report if there is still trouble after 3.1 is released tomorrow.