The latest version of this page is available online here. Check it for any problems discovered after this version of FoundationStone shipped.
There is a known problem with the postscript FoundationHebrew & FoundationHebrewScript fonts on Linux. One character (Chiriq) does not show up. This is the very last glyph (89) in the font, and should appear in position 0x2D (ie when the minus key is pressed). Download Font2DTest.jar.zip to see the problem. If you manage to fix this (probably using a WYSIWYG postscript font editor on Linux) please get in contact.
Another possible cause of the applications misbehaviour is a corrupt "FoundationStonePreferences" file. You'll find it in your home directory. Quit the application, delete the preferences, then relaunch it.
If you encounter problems with the auto update feature, it is suggested that you download the application again, and allow the auto update to run again.
Some useful tutorials:
Paul's Debian Unix How To.