IT makes sense that you would have more problems with your branch app because that is the app you are making the most changes to. The issue is that the Histograms related to some of the operational tables cause problems because they adversely impact performance when the FUA is trying to get the latest rules to load the rule assembly cache. With many people doing updates in that app and the app constantly recompiling, there is a ton of IO that is being slowed by an inefficient query plan caused by the Histograms. On our last project, compile and rule access times progressively got slower and slower until we disabled the histograms. Disabling the histograms improved performance by orders of magnitude.
Check out the following link for an explanation why:
IF it is an Oracle database, I have also had trouble (in 6x) with tables with Histograms enabled for query optimization. The Histograms caused our queries to run very slowly over time until we had the DBAs turn them off.
YOu could check with support to see if that is a possibility here.
Have you tried increasing the timeout value for your JDBC connector? If you run the query listed above in SQL Developer you should get an idea of how long it takes to complete. Then you can adjust the timeout value accordingly. In tomcat for example, you can adjust the maxWait parameter to increase the timeout value.