Ann Loraine please advise how you would like to proceed.
After further investigation the issue stems from a potential bug introduced in 8.4.0 which requires that each file in the quickload annots.xml have a title. Note that the title is currently listed as optional in the igb users guide. The quickload attached to this issue for testing does not include a title in the annots.xml for the 2bit reference. This is what causes the null pointer exception and failure to load any data in IGB 8.4.0 - 9.1.4.
If a title is added to the reference 2bit file in the annots.xml then no null pointer exception is thrown for IGB 9.1.4. The reference title will appear in the available data and be selectable. If the user selects the reference title and clicks load data the sequence will be loaded in the coordinates track. This allows for 2bit or fa reference sequence files to be remotely specified in IGB 9.1.4. If the 2bit file is available in the quickload then clicking load sequence will load the sequence in the coordinates track.
In IGB 9.1.6 the title is ignored and the reference does not appear in the available data.
The easiest resolution to this issue would be to make no further code changes in IGB, but update the users guide to state that the title is required. New quickloads that include a remote reference sequence will appear with a reference data option in the available data for versions of IGB less than 9.1.6.
It may be possible to edit IGB code to add a new XML root element, but this may require some significant code changes.