@PauloF
I followed the instructions on pages 2 and 3 of the READ_ME_FIRST_130.pdf document that came with the v1.30 operating system update. Steps 1 to 5 - ie, format media on FG, place two installation files on media from computer, place media in FG and boot, power off and remove media, boot up, factory reset. Done it many times now and have also downloaded the OS update from Roland's website again just in case the original download was corrupted in some way.
Everything appears to load properly during the initial OS update installation - ie, 74 samples, 900+ phrases, seven songs and numerous templates. If I reboot the FG without the USB memory connected, with the content only ever having been saved on the internal memory, the OS loads fine with all the v1.30 content in its correct place.
If I then perform a project 'Save As' operation to the USB media, creating FantomG001.prj it appears to go smoothly. But after rebooting the FG I find it invariably leaves out some element of the content.
I do think it's probably being saved, though. That's because each time the missing data will be different. If, for example, sample number 25 is missing the first time I reboot, I am likely to find no25 has been restored the next time I reboot but that no31, no 42 and no57 will be missing instead. The same thing happens with MIDI phrases, songs and studio templates too.
This suggests that the problem is arising at the booting stage and also when project loading, not when it's saved in the first place. It's as if the FG is failing to load some of the samples, phrases or whatever every time it boots or loads a project. But different data is affected on each occasion.