Version 1.0.9 on Ubuntu 9.10 (Karmic Koala), AMD64 2.4 GHz:

When exporting an application using Present Mode, only the top left section
of the sketch is shown.

Using the standard (Not Present) mode does not have this issue.

Another workaround: Using the JDK that comes bundled with processing
instead of the default JDK (java-6-openjdk) by placing a java symlink in
the current directory of the sketch, and modifying the sketch shell script
to call './java' instead of 'java'.

Code that reproduces this issue:

void setup() {
size(800, 600);
}

void draw() {
fill(0, 255, 0);
rect(10, 10, 700, 500);
}

Export application in full screen (present) mode, run it and you will only
be able to see the top left section of the sketch.

Is there a reason that the included version of Java was not being used?
Only Sun Java is supported:
http://processing.org/reference/troubleshooting/#linux