Just so I'm clear, does the original fob (the proximity one with the battery in it) start the bike when you put it against the front of the ignition with no battery in it? Or does it only work with the battery dead but in place? I have a 2011 model in case that matters.
Kawasaki sells TWO FOBs for the C14 and there are TWO different systems on the bike to unlock it. First the two systems are, in Kawasaki's terms:
1) KiPass
2) Key Immobilizer
It helps if you speak to them in THEIR terminology. KiPass is the ACTIVE 300MHz (in North America at least) system that will unlock the bike from a short distance away. When you press the stove-knob the KiPass ECU under the seat sends a radio signal that is picked up by the KiPass FOB. The FOB then replies and if the bike is happy with the reply, the ECU will unlock the bike. The Key Immobilizer system is different, actually completely different and independent and it ONLY comes into play if the KiPass system fails to locate a FOB and unlock the bike. The Key Immobilizer system is a very short-range RFID system with the transceiver located in the front part of the keyswitch housing. So for it to do anything you must NOT have your KiPass FOB around with a battery in it and must hold a Key Immobilizer device against the front of the keyswitch housing while you press the knob. The KiPass ECU sends a signal to the keyswitch to try to read a Key Immobilizer and if successful, it will unlock the bike.
Ok, once that's straight we need to talk about the FOBs themselves. As I mentioned, there are TWO.
1) KiPass FOB - This is the "big" FOB with the battery in it. But, and this is the part that trips up many dealers and C14 owners, there is ALSO a Key Immobilizer device inside of the housing. If you take it apart like you are changing the battery, you will see it in the larger end of the half of the case that does NOT have the battery slot. It's a small ( about 10mm x 2mm) black plastic bit that you might otherwise miss. This is a Key Immobilizer FOB device and if you remove it from the KiPass FOB housing it can start the bike all by itself. This is the one that the dealers never know to program and, I believe, is the one you are having issues with. (BTW, make sure your KiPass FOB has this inside. I suppose it's possible that it could have been removed at some point.)
This is also why you don't have to worry about getting stranded by a dead KiPass FOB battery since, as long as it's properly programmed into the bike, this will always start your bike in a pinch. You take the key out of the FOB, place the empty slot where the key was over the top of the keyswitch, and press the knob. The bike will unlock. Try it but you must remove the battery first, otherwise KiPass will unlock the bike and you'll never test this function.
The KiPass system uses IDs that come ONLY on the plastic bags that come with a new bike or with a new FOB from Kawasaki. As far as we now know, it's NOT possible to recover this ID if you don't have the bag with the label. So an ID-less FOB is nearly useless. You can repurpose the Key Immobilizer chip but nothing else. But you MUST have the ID for the FOB if you want to program a KiPass FOB into your bike. No ID, no programming! This is also why you are stuck if you lose all your FOBs. You cannot enter programming mode if you cannot unlock the bike. So you must buy a new KiPass ECU that comes with a FOB pre-programmed into it to revive your C14. NEVER KEEP ALL YOUR FOBs with you. Leave one at home or in a safe-deposit box so that if the worst-case scenario happens, you can (eventually) get your bike started. If you bought a used bike with just the KiPass FOB, remove the Key Immobilizer chip and leave it home until you get a spare! I personally have one KiPass FOB and TWO Key Immobilizer FOBs. I use the KiPass for daily rides. If I'm going on a trip, I pack the Key Immobilizer, usually in an inner-pocket so I can get it in a pinch. I always leave the 2nd Key Immobilizer at home so that I have a fail-safe backup if everything gets lost or stolen.
The ECU has 6, and only 6 slots for these FOB IDs. A new 2010+ comes with ONE slot programmed. 2008-2009 come with TWO FOBs and TWO slots programmed. You CANNOT EVER re-use a slot, you can only erase/deactivate it. Once you've written all 6 slots, no more KiPass FOBs can be added. The KDS system does show you which slots are available and used but it DOES NOT show you the IDs in any slot. So you cannot recover IDs using the KDS system. (I have a suspicion that there is a way, but it's currently unknown to the public.)
2) Key Immobilizer FOB - this is the small "credit card" FOB (although it's a lot smaller than a credit card) and this contains ONLY a Key Immobilizer device and a space for the tiny "spare" key. The Key Immobilizer system does not have any printed ID that you must know. Once you enter the Key Immobilizer programming mode you place each and EVERY Key Immobilizer FOB you want to use, one at a time, above the keyswitch, and it will read and record the IDs. Once you have read all of them, you tell KDS to program the Key Immobilizer and it will REPLACE whatever is in the ECU with the new set of IDs. From that point on, only those ID will unlock the bike. This is why you MUST RE-PROGRAM ALL YOUR Key Immobilizers every time you want to add one. (Dealers, for some reason, just can't get this!)
So this is why the KiPass FOB is tricky, if you buy a spare, you need to have BOTH parts of it programmed into the bike, as well as all your other Key Immobilizer FOB devices to have a complete set of working FOBs.
I hope this helps your understanding of what's going on. IMHO there is little excuse for a dealer not to know how to do this. It's all clearly documented in the KDS Users Manual, which they have! There is absolutely NO excuse for the Kawasaki Service Technical line folks to not know how to help their dealer out.