It appears that you will have to start from the beginning. Offhand the only way I can imagine that the throttle is affected by the flap switch is that you had a program mix of some kind. When you reset the program, it erased the mix.
On all JR transmitters starting with the 9303, the proper way of setting up dual surfaces in the ACRO mode is through the WING TYPE menu. For ordinary circumstances, never use a program mix! On the 9303 before you can use the WING TYPE menu to set up dual flaps, you have to make some other decisions that involve both the DEVICE SELECT and the WING TYPE menus. The reason for this is that the transmitter picks certain channels for the ailerons depending on the wing type and you have to pick other ones for your flaps.
Channels one through four are your primary channels controlled by the sticks and can only be altered with effort. Channel two is the aileron channel. If you have only one aileron servo, this is the channel you would use for both ailerons. If you have dual ailerons then channel two is your right aileron for both the NORMAL and FLAPERON wing types. It is the left elevon for the DELTA wing type.
The FLAPERON wing type is for a conventional wing with dual ailerons that can function as flaps but has NO discrete flaps. If your plane has one or two actual flaps, you must use the NORMAL wing type. With the FLAPERON wing type, the left aileron is on channel six, the FLAP channel.
With the NORMAL wing type and flap(s), the right flap will be on channel six. The left aileron and flap can be on any channel that is not being used.
The procedure for setting up your plane is this:
1. Reset the program
2. Decide on a wing type and if you have actual flaps set the WING TYPE to NORMAL in the WING TYPE menu
3. In the DEVICE SELECT menu, INH the outputs of all the channels that you will not be using, possibly GEAR and certainly AUX2 and AUX3. (AUX4 cannot be used in the next step.)
4. Return to the WING TYPE menu. On the bottom is the dual/mate. Select the INH under FLAP and press the roller. You can select any channel that is not being used for the left flap. Using AUX3 for the left flap has the extra benefit of letting you trim it independently of the right flap using the AUX TRIM switch.
5. If you have dual ailerons, set up the left aileron as you just did for the left flap using one of the remaining unused channels.
Allan