In Windows try deleting both the AVs (in Modules/Bible folder) and Strong's modules, plus the strongs .idx module (both in Modules/Dictionary folder). Then extract the files from your ba-study+.tar.bz2 archive you downloaded and put them back in the respective folders. If it works, do the same with your Linux installation. The .idx file in generated by Bible Analyzer. It is not in the archive.
If you want the Windows installation file of the Study bundle (will install in the right folders automatically), email me and I'll send you a link.
Developer, Bible Analyzer
But to him that worketh not, but believeth on him that justifieth the ungodly, his faith is counted for righteousness. (Rom 4:5 AV)