Make sure the input dataset has the metadata "database" assigned.
The genome mapping indexes for this tool are sourced from UCSC. So, only databases sourced from UCSC will work with the native indexes.
Note that at Galaxy Main (http://usegalaxy.org), not all indexed UCSC databases have liftover indexes. Our data procedures have changed and updating to include all available files is on the short list for new data additions. Follow progress here: https://github.com/galaxyproject/galaxy/issues/1470
Meanwhile, if your UCSC genome is not available/indexed for this tool (yet), you can use the Batch Coordinate Conversion utility directly at http://genome.ucsc.edu. This tool does not have a direct Galaxy import function, but the output can be downloaded from UCSC then uploaded to Galaxy.
Thanks, Jen, Galaxy team