First: I don't have screenshots comparing 1.3.5 to 1.4.1 which may be the most helpful. However hopefully I can cleary articulate what is the matter.
For example, the following line is rendered differently from 1.3.5 to 1.4.1:
'I maintain a WSRP4J source code tree in Subversion since WSRP4J has no formal releases or release cycle.'
In 1.3.5 the text 'WSRP4J' was not treated as a CamelCase link. In 1.4.1 it is.
Another example:
'MSE trunk - may contain MSEL customizations and is copied from https://bajor.mse.jhu.edu/repos/public/trunk/apache/portals/wsrp4j/20050418.'
In 1.3.5 'MSEL' wasn't camel case, in 1.4.1 it is.
Another example:
'Based on experiences it seems best practice to upgrade to the latest and greated Pluto Portal Driver and Pluto Portlet Container. This is especially true if you require Servlet Spec 2.4 and JSP 2.0 (for JSTL enhancements).'
In 1.3.5 'JSTL' wasn't camel case, in 1.4.1 it is.
It seems like words in all caps are considered camel case in 1.4.1 and they were not in 1.3.5. Can the behavior be reverted? I'd be happy to test a fix for you.
The CamelCase link parser no longer turns ALLCAPS words into links.