Actually we've had no problems interchanging and cross connecting Futaba's with JR's and vice versa, however there are a few "gotcha's" if you are not aware of them.

e.g.

Typically with a JR to JR connection the Master TX is flipped "on" while the slave is not.

With a JR to Futaba, with the Futaba as the slave, the Futaba must also be on.

Trims, throws and direction must be set identically with both radios before interconnecting them.

Both radios must be in PPM mode.

etc.