I have come to find out that fade in and out cannot be saved in a registration! So no accidental storing with fade out, could be the issue.
Although the Fade In/Out function (or it's settings) can't be directly saved in a registration, it can be assigned to a foot pedal, and the pedal assignment can be saved in a registration if the 'Pedal' group is checked when the registration is memorised.
If you have not intentionally assigned the Fade In/Out function to a pedal, you may have a registration bank (possibly from a third party) which contains the pedal assignment set to this function. If you load the bank and select a registration button that includes the
pedal assignment, this will be changed to whatever function is in the reg. (presumably Fade In/Out!).
Once a pedal assignment is set, it will remain set until you change it, either manually, by a registration, or by turning off the power (on all models except Genos, the pedal assignments are lost when the power is turned off, and default assignments are restored when the power is turned on). So if you select a registration that changes the pedal function to Fade In/Out and do not realise that the assignment has changed, then without turning off the power, save another setup to a registration button with the Pedal group checked, you will unwittingly include the Fade In/Out pedal assignment to that reg.
You can prevent registrations from changing the current function assigned to pedals by checking 'Pedal' in the Freeze table and turning on Freeze using the panel button before loading the offending reg.
You say that you have resaved registrations with the Pedal group unchecked, but by this do you mean individual registration button memories or whole registration banks?
If it is the latter, then this will not work! You must change and memorise each affected button memory in a bank before saving the whole bank. The groups checked in the Group Contents table only determine what is memorised in individual buttons and have no affect on what is saved when you save a whole bank.
If you are still having problems, why not post one of the offending reg. banks that you have attempted to change, and someone can take a look at it.
Regards
Ian