I found a solution a day or so after making this thread, but didn't think to
post about it. In case someone gets stumped by this in the future, or just
wants to see what the problem is, this post is for you. :)
I pinned down that whenever I opened something with window decoration, this
would make the panel completely hidden. That seems very strange to me, and I
wonder if I should file a bug report. Well here's how I found the lost panel:
Open the terminal (ctrl + alt + t), and enter in sudo apt-get install compiz
ccsm if you don't already have compiz (if you don't know what this is, you
likely don't have it) run ccsm, and uncheck the box for window decoration,
then in the terminal, enter in compiz --replace to use compiz as your window
manager until the end of your session Now, hold down the Alt key and right
click on the panel, open properties, and then restore the position of the
panel Finally, remember to re-enable window decoration! If you don't want to
use compiz until the end of your session, run metacity --replace
