Is it the ECU or up by the stove knob? 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. Trying to figure out what's between the bike and the fob that's possibly blocking or interfering with the signal.

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).

https://forum.concours.org/index.php?threads/hacking-the-c14-kipass-ecu.25644/

I recently got booted off the COG forum under their new bizarre rules - but I'd previously saved the above for a rainy day's question.   

I had the same problem b72b 18 months ago.  If I squeezed the fob it 'came back.'  This happened over some months until one day no amount of squeezing 'found it.'  After I'd stopped I had to use the passive part of the fob on the ign lock to get going again.  I took the fob to an electronics repairer who found under magnification that there was a crack in the solder of a tiny transistor.  On second attempt he found the correct size part.  He had to buy a strip of 200 of them to get 1 - $20 the lot.  So $35 and a few weeks later I had my fob back in new condition.  I used the half credit card size passive immobilizer fob key thingy in the mean time.

LOL!  I thought it was wiggling the knob, not the FOB   I get an "F" on in-context reading in this case.

So, it could also be as simple as a poor battery connection in the FOB; cleaning and "re-springing" the contacts could be helpful.

I have replaced the battery recently...
Seems it doesn't do it as much or at all when it's in my pants pocket. I wonder if the Corbin seat has anything to do with it.
More experimenting is in order.... means more riding!

The KiPass receiver and antenna are in the KiPass ECU which is the black box you see right under the seat.

It's often confused with the FI ECU which is behind it.

So it's plausible that the Corbin seat, which I believe has a metal seat pan, may block the signal.

Yes, there are 4 black boxes under the seat.  The one with 3 plugs is the relay/junction box; the one with 2 plugs is the EFI ECU; the one with 1 plug is the KIPASS ECU; the one with no plugs is the tool box.   

The link to the COG forum above has the fob antenna shown within the KIPASS ECU. 

So it's plausible that the Corbin seat, which I believe has a metal seat pan, may block the signal.

https://www.corbin.com/care2.shtml

"Saddle Base: The Corbin Fibertech basepan"

Fiberglass.  Might be a bit less transparent to RF than stock, but probably not by much.

Nah, I have a Corbin 2-piece seat and my Fob works fine from my jacket pocket.
If manipulating the fob itself fixes the problem then you most likely have a damaged fob, assuming that you have replaced the battery with a known good battery.
Yet another area where the 08-09 are superior. <Smug mode on> We got 2 FOBs. 

Yet another area where the 08-09 are superior. <Smug mode on> We got 2 FOBs. 

We gen 2's get two FOBs also, it is just that one of them is passive RFID only.  I will never really understand why they did that, though.

Nah, I have a Corbin 2-piece seat and my Fob works fine from my jacket pocket.
If manipulating the fob itself fixes the problem then you most likely have a damaged fob, assuming that you have replaced the battery with a known good battery.
Yet another area where the 08-09 are superior. <Smug mode on> We got 2 FOBs. 

I've had 2 Corbin 2pc seats and never had any issues with the Fob connecting from my pants or jacket pockets.

I have no issues with the Corbin seat and the FOB as well. I carry the FOB in my pants pocket, or jacket pocket, it makes no difference.

I've had issues with mine on the Indian.  I've started to carry it attached to my belt.  Seems to work better that way.

I had problems carrying the fob near my phone.