@kaz69 No, only one OS boots at a time. Nothing additional is running in the background from the other installations. Not sure if PINN asks or allows you to set the partition sizes but obviously it would be handy to have larger partitions for those OSes that need it.

Pi Model or other hardware: 3
Power Supply used: CanaKit 2.5A Micro USB Power Supply with Noise Filter
RetroPie Version Used 4.2
Built From: Flashed retropie to work through Jessie, made a disc image copy to place onto new (not working) micro sd
USB Devices connected: keyboard, ps3 controller (via bluetooth)
Controller used: ps3
Error messages received: none - system stops during boot
Log found in /dev/shm/runcommand.log (if relevant):
Guide used: youtube install instructions
File:
Emulator:
Attachment of config files:
How to replicate the problem: plug in retropie to turn it on. system stops during boot process.

All, finally home from my work trip and I updated the rpi-clone tool and it worked perfectly. Thanks for the tip on the new update.