This article sounds promising.
Both XDebug and Eclipse (in its php dev env) can use the DBGp protocol by the look of things. Based on that article, you might be able to get things working by messing with Apache’s .htaccess file[s], or by running a DBGp proxy (whatever that is). Further details in the article.
I suspect both XDebug and Eclipse are connecting to the same PHP debug session, stepping on one anothers toes, causing Hilarity to Ensue.
That or “undefined behavior”. Either way.