Registrations on x1 are best stored in what is called single registration mode because if they are done in "block" mode the same thing happens as is happening to you. Block mode simply sets things like tempo style etc whereas Single regs store all settings(almost).
Single regs are stored on Hard disk and are accesses when a button called Registrations is lit(pressed).
Perhaps you have similar system in 2000 KB ??
Some setups are only saved if saved as "power on Settings" - I have to press SAVE and select "power on setup" and save.EG pedals setups , midi setups.
I hope this leads you somewhere????Pierce