My workaround is to ignore this since my results still appear correct and users don't see this but what does this mean? This message is showing up in my Java console, using the fop 0.95, when I send the output to the org.apache.fop.render.awt.viewer.PreviewPanel with embedded code running in webstart. (I can't use fop 1.0 because it had a problem which actually did affect the appearance of the output)
org.apache.fop.fonts.FontCache loadFrom WARNING: I/O exception while reading font cache (org.apache.fop.fonts.FontCache; local class incompatible: stream classdesc serialVersionUID = 605232520271754719, local class serialVersionUID = 605232520271754718). Discarding font cache file.