Turns out you can't have commas in the name of files being copied to FlashScan/AutoCal. I originally thought it must be a limitation of the FAT32 file system implementation that is used on the devices, but FAT32 can have commas in file names. The actual problem is the filename and open/create parameters are passed from the PC to FlashScan/AutoCal using a comma separated list.
For example, creating a file called "file.txt" is passed to FlashScan like this: "file.txt,w+", where "file.txt is the name and the "w+" that follows the first comma tells FAT32 to open the file for writing and if the files does not exist to also create the file.
Unfortunately if you have a file name like this: "name,with,commas.txt", then the parameter that is passed to FlashScan/AutoCal becomes: "name,with,commas.txt,w+". That is interpreted by FlashScan/AutoCal as filename="name" and open/creation parameter= "with,commas.txt,w+". Which obviously doesn't work.
For now, don't use commas in filenames. I'll investigate fixing it in a future release.
Regards
Paul