Saxon performance difference in eClipse and App Server

Saxon v9.1.0.6
Input XML size : 30K
XSLT size: 33K

When I run an XSLT as a standard Java application in eClipse I get
very different perfromance than running exactly the same piece of Java
within an App Server.

In this case I am running an XSLT2 stylesheet that validates a
message. The XSLT was generated from a schematron schema and works
successfully in both situations.

The Java code caches a Templates object for the stylesheet to improve
performance, and indeed this is evident in both sets of test results
(i.e. the first time through there is an overhead for reading the XSLT
from disk and caching a Templates object and thereafter this is very
much reduced as it is retrieved from cache).