I had this problem with my Stomp on 3.6 and 3.7. Everything else worked fine (Edit, HXFX, and Native). The fix was to download the update from my iPad and copy it to my Mac. Opened the Line 6 Updater app and selected the file. Worked fine.
I’m using a TRS to TRS cable with mine. Try this:
Connect a TRS cable from the Stomp EXP/FS jack to the SP1 Out 1 jack.
Press the PAGE left/right buttons at once to go to the MENU.
PAGE right once and select Global Settings.
Upper Knob scroll to Preferences.
PAGE right once.
EXP/FS Tip = EXP 1
EXP/FS Ring = FS5
Tip Polarity = Normal.
Press VIEW to exit the MENU.
Go to the Preset Edit View.
Make a Wah or Volume Pedal block (you can only have one per preset).
Press the PAGE left/right buttons to the MENU.
Select Controller Assign.
Param = Psition
Controller = EXP 1
Press the PAGE left/right buttons to the MENU.
Select Bypass Assign.
Switch = FS5
Type = Latching
Press VIEW to exit the MENU.
Save the Preset with the block off.