Is it the ECU or up by the stove knob?
I am not sure that question has ever been posed (or at least answered, authoritatively) before- exactly where the antenna is located for the active RFID. It is likely either under the seat, or near the ignition, like you speculate. But I don't know, and I don't think the manual says.
When I ride I usually put the fob in my riding jacket chest pocket. Sometimes it says 'fob lost' and if I reach up and wiggle it, it comes back.
Wiggling the stove knob is not a factor- it is more likely just the repositioning of your body + time.
Trying to figure out what's between the bike and the fob that's possibly blocking or interfering with the signal.
That question HAS been asked before. The response is usually either the active FOB battery is getting low and/or there is interference present near the bike. I suspect the latter. It is rare, but I have had this happen to me maybe twice in 10 years, neither was due to a low battery. I always keep the active FOB in the inside, velcroed, lower-chest pocket of my riding jacket. It is almost never removed, unless it is time to replace the battery.
Standard practice is to perform an elimination trial, which might not be easy, especially if it is intermittent, or involves things not easily eliminated (like HID ballasts).
