Increase in ws.reputation.1 risks since deploying 12.1.4

We recently upgraded our SEPMs to 12.1.4 (Windows 2003 r2 x86 servers)  Last Thursday I began deploying install packages to a subset of our environment and since we have seen an increase in reputation violations.  At first I thought it was just the Prism application, that something had changed in the program that caused it to become an unknown.  However I have been seeing others.  Was wondering if anyone else has seen this behavior in 12.1.4.  Does it use the same reputation database as 11.0.6?