Let me see, it happened a couple of times and keeps happening. When I shut-down JBoss AS, then do some editing and thereafter start up JBoss AS again, it correctly says "x filed modified in module ..." where x is the correct number (e.g. 1 or 2).
What else... maybe some special is that I have two JBoss AS instances configured, and thus two run time servers defined in Eclipse. The second instance hosts a kind of messaging hub where the main app connects to via JMS, I don't edit this one often. This second instance has another set of ports defined.
Other than that we're using MercurialEclipse. Something odd with that is that the directory in the workspace that comes from Mercurial is my_main, which contains the ear project my_main, my_main_ejb and my_main_web. Eclipse only gets to see those 3 nested directories, but not the parent folder.
so the structure is:
workspace
my_main
my_main (EAR project)
my_main_ejb
my_main_web
This is maybe a little weird. But I'm not sure it's related. Other than that I can't think of anything special. I just upgraded from Java6u21 to Java6u23, but this didn't make any difference. Let me know if there is anything specifically I can check.