The problem is described in the ROOT forum in the post linked below:
When configured with -Dgnuinstall=ON, CMAKE_INSTALL_SYSCONFDIR is <prefix>/etc/root/, and ROOT ends up looking for the PCH in the wrong location, since it uses a hard-coded <prefix>/etc/ instead for the same directory. ROOT fails to start in this configuration, with the error shown below:
The PCH is not found because it's installed in /usr/local/etc/root/allDict.cxx.pch.
To reproduce this issue, one needs to configure ROOT with -Dgnuinstall=ON, build, install ROOT with make install, then try to start ROOT.