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Tried another card today.... Retropie installs and boots, then after adding roms I get the dreaded "garbage" message.
I added roms this time with Emulationstation off, and rebooted.

For anyone else that is having this issue i have discovered the solution.
install retropie 4.0 rather than 4.3 and simply update the setup software from on the pi rather than when mounting the micro sd card.

I have found a solution. simply install 4.0 rather than 4.3 and update the setup software on the pi after first boot