Sounds like typical production woes... keep at it Mike!
Thanks Jim. Nothing unexpected - especially with Chinese suppliers. I deal with this sort of thing in my day job, but it's even less fun when it's your own toy.
"* So boards without the new bootloader works out of the box but without the features of said option?"
The revised bootloader code works on both old and new boards. It hasn't been shipped yet as it is part of the new firmware. The change is to correctly set up the internal memory controller as a result of an errata.
"* This new batch of ARM cpus only has slightly slower flashmemory write cycle? not slower flashmemory read accesstime?"
it's still in spec - just the old chips worked with the faster setting. It's only really read that's interesting from the flash in our case

"* Does the dead 1.2 V supply mean that you have to check and replace this on all boards?"
All power rails are checked on each board as part of the test suite. If it's out of spec the regulator is replaced.
"* How is the DDR memory self calibration going?"
Done, works like a charm.
"Whats VNC2?, If I recall it correctly, the ARM cpu is the USB-host and sends this to the FPGA via i/o. I like the everything-on-one-board-solution Perhaps an option would be to handle other USB devices by just forwarding the raw data and let the Amiga side deal with the configuration of endpoints etc."
This ARM cannot be used as a USB host. The VNC2 is an optional module which fits on the board instead of the PS2 connector and provides two USB host ports, and all the software muscle to drive them. It speaks mouse/keyboard SPI back to the FPGA which feeds it into the Amiga core.
"What I would like is to be able to just plug the board via USB ethernet to the local network and run with it, without messing with any pc-2-sd-2-arcade-repeat. Firmware updates would be just a matter of pressing a key. "
You can with the ethernet adapter on the daughterboard.
Firmware updates for the FPGA are as simple as copying the file on the SD card.
For the ARM code you push the menu button while powering on the board, and run an update program on your PC. The two will talk, the ARM flash is reprogrammed and you are good to go.
You can also update the bootloader this way too.
If you mess it up, there is a link on the board to reload a default boot loader.
/MikeJ