Most probably the issue with JAR has a different nature: for example the font .JAR is packed to .WAR, and the web application is not configured to be unpacked to a work directory. In the case PD4ML may have (not in every configuration) fail to load resources from .JAR

But the issue with c:windowsfonts tells that the Tomcat instance #2 has a configuration (or inconsistence) problem. I would start with a resolving the issue.

Enable debug info on both instances and compare PD4ML’s diagnostic output. Is it identical by identical PDF conversion requests (except the failure messages)?

Also requested PDF samples (from even blank HTML) would give us some additional info.