Jazz annotate command (Blame) timing out when being called by SonarQube analysis

Question

I am currently running SonarQube v6.0 with RTC Jazz plugin v1.1. I am running analysis on a MVC web appliation project that is ~700k lines of code, ~5000 classes and ~6000 files. When I enable the scm sensor the Jazz Annotate calls are taking a long time. I have enabled the detailed logging and you can watch them request/respond and while watching they seem to take 5-20 seconds each. Eventually the job runs for 3-4 hours and one of the annotate calls (seems random each time it has failed) takes longer than the 60s hard coded time limit allowed for Blame in the plugin code. I have engaged our network support team and connectivity between our rational instance and the build machine issuing these commands was 5-10ms each so I don't think its network. I have also issued SCM (and LSCM) commands from that machine requesting the same type of info manually and it seems quicker, but not quick enough (a 3-5 seconds roughly)

What can I do to speed up the Annotate calls or determine where the bottleneck is?