Chris,
I uninstalled PB 12.6 and then reinstalled, runtime packager was correct and enabled. I then just applied the latest EBF, build 4088 and it looks correct also. So not sure if it was something caused by upgrading to another EBF or not but see if that works for you. I also made sure on both autorun.exe to initially install and then setup.exe with the EBF, that I right clicked and ran as administrator. It looks OK to me now and does build the msi . I was seeing exactly what you were seeing earlier.
Pat