This happens with lxr 0.9.2, running under perl 5.6.1.
Setting the "virtroot" variable, which contains the
local part of the lxr base URL, to '/' in the
configuration file (lxr.conf) when lxr runs from the
top-level directory of a (virtual) host results in
generated links not working anymore; for example, an
expected link target of
"http://source/src". Setting "virtroot" to '' (empty
string) instead solves the problem.