With the release if 6.3.1.x and higher the HSQL database was updated. This upgrade requires us to check each of your HSQL database files in \stoneware\hsql and upgrade the format to a newer storage method.
It does this by reading the data from each hsql .data file and writing it to a new file then swapping the files upon completion.
The HSQL engine is not enterprise grade and was meant as a simple database to test a feature that needed a database without having to set up MYSQL or MS SQL. Because of this sometimes the HSQL .data file can become corrupt or grow so large that the upgrade process can not upgrade the HSQL database and gets "stuck".
Before upgrading from a UW version below 6.3.1.x please check for these two things.
If you have either of those two scenarios please contact Stoneware / Lenovo Software support to discuss your options for disabling/resetting those databases prior to running the upgrade.