I had the same issue with RC1 of OS 16. I would use the hard reset, or even press the reset button on my frontloader NES, and it would come up with "OS Init..." and just hang there. With the full release of OS 16 I no longer have the issue. I also completely formatted the SD card (no quick format) and copied over the full directory structure in one block. (E.g. i made a folder with the EDFC folder and ROM folder and copied that over at once instead of copying file by file). So a completely and fully defragmented SD card seems to work.
ONLY issue i now have is with FDS games. i like the auto disc swapping, but would like to be able to turn that off. With the way the OS functions right now, you will never be able to see the full intro to games like Zelda, Zelda 2, Doki Doki Panic, etc. since the OS automatically swaps disc sides before any inputs are given. I would like to have it so that it will automatically switch sides once i press start or some other button combination.