When upgrading from an earlier version of RPT, I ran into numerous issues. See article "https://www.ibm.com/developerworks/forums/thread.jspa?messageID=14931802&".
I had both RPT and RFT in the same program group. While previously not recommended, there was nothing I saw/read that prevented this. Infact the IM allows you to put it in the same location. It turns out that the latest software seems to cause conflicts and possible upgrade failures when they are co-located.
Everything from project corruption, licensing race conditions, JVMs not starting, loader errors, etc occurred in my situation. Once the RPT and RFT were uninstalled and re-installed in separate program groups (folders SDP, SDP_1), most of the issues disappeared.
I still had 1 issue in the size of Heap setup in eclipse.ini for RPT. Mine had a value -Xmx1200m. I needed to change this to -Xmx1024m in order for the JVM to start. This was located in c:\Program Files\IBM\SDP_1\eclipse.ini. Note, my test systems had 3GB of RAM so it is not clear why it could not start the JVM.