I'm so far not able to duplicate your bug from the video, and I'm still not completely understanding your set up.  Are you assigning each Aux Switch button to 2 functions?  As in, is a button that is assigned to Pre+ also assigned to a Looper function?  Will you detail your exact Aux switch set up from the system mode?  For example: 

TIP has Pre+ AND PLY

RNG has Pre- and Rec

T+R has FS1 and STP 

Also, make sure you are using a TRS (or stereo) cable with your Aux Switch.  A mono cable will not work.  

Either way, we never designed the Aux switches designations for Looper to be overloaded with something else, so we can't make any promises as to how this will or should behave.  It honestly never occurred to me that it could be used this way.