For example:
I set 'Base Class Path URL'=/a/
and enter 'Base Filesystems URL'=/a/. After that I
will get a message "There can be conflicts in
mappings ..." It's OK.
After that I enter 'Base Javadoc URL'=/b/ and get
the message about conflicts although /b/ is
correct value.
I suppose it's because all three fields are
checked with each other. 
I suggest to check only a last entered value (e.g.
if I entered 'Base Javadoc URL' then check it with
others but don't check 'Base Class Path URL' with
'Base Filesystems URL')