Java XML : The Sum of all nightmares!!

Hello there! This is keeping me from sleeping at night :(
I'm using Xalan to perform some XSL Transformations. My project is
deployed inside JBoss 4.2 and I'm using JDK 5.0.

When the flow is run inside the container (for instance, we poll a
database, convert it into xml and then use a chain of transformers to
validate, enrich, transformate the whole message)

It works fine. But, when I run a test case from outside the container,
passing a xml that was created from a different document builder then
the one inside jboss (all transformers fail to transform) they simply
drop all tags from the xml.

I've already have a problem with validation and Xalan because of using
diferent document builders. I just can't understand why 2 xml files
that are identical are treated differently from the parser.

Please, is there a way of solving this?

Regards