I am not sure if what I am dealing with is my own inability to find the correct configuration option, or this is an actual bug.
I purchased the PragmataPro font for development purposes. I purchased the regular version of the font along with the Bold version. I did this so that when the font was in bold it would still be monospaced with the standard weight font. PhpStorm seems to be ignoring the fact that a PragmataPro Bold font is installed on the system and is "bolding" the font itself. This means that its spacing is not consistent with the regular font.
I am evaluating PhpStorm on Ubuntu 12.10 and Mint 14. I have tried both OS's in VirtualBox vm's and on physical hardware with an nVidia video card. In the case of the vm's I did not change video drivers but on the physical machines I did try several version of the proprietary driver. All of these combinations resulted in the same behavior.
If anyone has any insight please reply.