In the remote THREDDS catalog presentation code (primarily XSLT) the links produce contain double "/" characters. This is probably an issue in path construction the the threddsCatalogPresentation.xsl (most likely) or in the threddsDatasetDetail.xsl (less likely)
It is possible that the java code (in StaticCatalogDispatch.java) is passing in garbage, but preliminary examination indicates that is not probably the root cause.
This should be tracked down an corrected.