Searching for a URL such as "http://redmine.nscontext.eu/issues/show/2899" in an issue's comment (as well as other fields probably) is broken in JIRA 4.0. In JIRA 3.13 searching for the URL above would have yielded results.

This seems to be caused by the Lucene upgrade in JIRA 4.0.

There's a difference in the queries being produced:
JIRA 4.0
+body:"http redmine.nscontext.eu issu show/2899"

JIRA 3.13
+(body:http body:"redmine.nscontext.eu issu show/2899")