If you select TrueType (TTF) fonts without setting a font name, PHPlot fails to find a font on Ubuntu. This used to work.
Starting with Ubuntu 'precise' (12.04), they changed the install path for the LiberationSans-Regular.ttf font that PHPlot uses as a default. In /usr/share/fonts/truetype/, it used to be installed under "ttf-liberation" and now it is under "liberation". See changelog.Debian entry for 1.07.0-2.
The change didn't break anything using fontconfig, which finds the fonts anyway, but PHP doesn't use fontconfig. So PHPlot no longer finds the font.
This has been fixed and committed to SVN (on the /Rel6 branch). Added "liberation/..." to the search path, leaving the old "ttf-liberation/..." there. The fix will be in PHPlot-6.0.0.
Updated documentation: "TrueType Font Selection" and "Default TrueType Font" in "PHPlot Concepts".
Note: I decided not to change the order of fonts for Windows. Currently, LiberationSans-Regular is first, then Windows fonts (Verdana, Arial) and Helvetica. The problem with this is that the default font used on Windows changes if you install Libreoffice (which includes Liberation fonts), because instead of using Verdana it uses Liberation. Although this is unexpected behavior, I do want it to use Liberation fonts on any system if present, for consistency, so in this case the unexpected change is considered the lesser evil.
Fixed in 6.0.0