This is a comment/work-around for FOP-3042 (as I have no JIRA account). By turning off support for complex scripts, the PDF renders correctly (and issue is "resolved"). Verified in FOP 2.6 & 2.8, both of which still break if complex scripts are enabled. Example configuration line to enable this work-around:
<complex-scripts disabled="true" /> Don't know why this is, but I guess it might explain why I never managed to replicate this issue in Batik (without FOP). Best regards, /Per