The crack program says that a different hex value should be used for 4GB games. Do you think it's worth updating your guide just in case people missed that part?<SNIP>
OK, I can also confirm that even though you don't write games to your microSD with EEPROM = "YES", the Sky3DS still keeps those games as the first 10. These games will remain skip free, but all other games added will skip, no matter what variety of template, EEPROM YES/NO, DiskWriter version, etc.
Thanks for confirming this for me. I had a feeling that'd be the issue you were having.