I managed to find some of your old threads here and on shapeoko.com. My problem seems like it is the same as you experienced, the grbl0.9 install works fine but the bootloader seems to be non-operational for some reason, maybe at some point they were sending out v2.2s with broken or non-existent bootloaders.
Are you just using a standard Arduino bootloader, or is there a custom one required for the shapeoko boards? Any hints/tips/links that might be useful in replicating what you did on my system? I’m a software developer and have experience with embedded systems (ARM/freescale, primarily) but not a lot of Arduino experience (and what little I’ve done with Arduino was years ago), so I don’t need a ton of micro-handholding but any info that can jumpstart me on the right path would be much appreciated.