Thanks to Felix Homann hint to look at...
http://support.wolfram.com/mathematica/systems/linux/interface/fonterrors.html
...I solved the error message from mathematica. The origin of the problem
was that I had over 3522 fonts and the setting in...
/usr/local/mathematica/SystemFiles/FrontEnd/TextResources/X/Specific.tr
...for @@resource maxForXListFonts was set to 2000. Once I bumped
that up to 4000 the problems disappeared.
Jack
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