@herb_fargus Thanks for the reply.
Yeah, coming from a MS DOS/MS Windows background I'm certainly not a linux expert so I'm constantly being surprised at the small nuances here and there. I suspect formatting as EXT2/3/4 would help, but that would defeat my purpose of then having it easily readable/accessible on my desktop (which is non-Linux). :)
I did hack away with OSX Fuse this morning to read a EXT4 partition from a previous backup of mine on a Macbook (it seems the retroarch update must have either removed the previous shader folders I had, or changed their locations, so I'm going to copy them back).
I had mounted this manually from back in 3.6/3.7, and it has always worked perfectly asides from these chown errors which I take are par for the course using FAT32 in the current set up :)
No big deal anyway, it's always fun. Thanks everyone!