Apple introduced System Integrity Protection and it interferes with where QTR installs the profiles. Basically, apples says that if you have an application that needs to write files to the system it should really be done in specific directories. They then fenced off some system directories for Apple only stuff to prevent malware from being injected into running processes. The downside is that it messes up some other really cool stuff you have been able to do with some third-party software (which is also where QTR has always put its profiles). The profiles (and other files not sanctioned by Apple) have been moved here: /Library/SystemMigration/History/Migration-(some UUID)/QuarantineRoot/.
There is a way around all this by booting into the recovery partition through the command line, turning off SIP, and then using QTR like normal. Just search for disabling system integrity protection and you will find a a bunch of explanations about how to do it.
Lots of developers updated their applications to work with this during the three month beta period, but QTR being shareware and made by a solo developer means it doesn't have the resources that larger applications/companies can throw at these kinds of updates. As much as I want to upgrade to el cap, I am holding off until Roy gets QTR working with it (without needing to reboot into an older OS or doing a round trip to the recovery partition and disabling SIP.
Hope that helps,
Richard Boutwell