I had this "KIPASS" experience the first week I had the bike. On Sunday, stopped to fuel the bike and went to start up. Click....message "IMMOBILIZER ERROR", then nothing. Several tries result in either "IMMOBILIZER ERROR" or nothing. After about 50 tries, give up, call the wife to bring the truck, load it up and take it home. At home, trying to decide to leave it loaded and take to dealer during the week, or take it off and check it out. Electrician in me can't stand it, so I unload it and push it in garage to check it out. Pull the covers and pull out the battery, the negative post is finger loose and covered with white grease (good thing if it was tight). Tightened up and problem gone. No more problems since then.
But, this and reading all the posts make me leery. Check out spare fob key, works fine when placed in correct position. Bought a spare spare FOB and get it programmmed, works fine. To see if the big fob would work with a dead battery, I remove the battery and try it like the spare fob.
I get a "SUBKEY ID ERROR" which according to the shop manual means " The sub-key of the other motorcycle is used or the transponder is not registered"-action or remark- "Check that the serial numbers of the FOB key and KIPASS ECU are agreement".
Don't understand why big FOB works in RF mode but fails using the chip only. Side note, Chip in big fob is in the plastic cover, not on the circuit board inside the FOB.
Just like my vehicles with regular keys, I keep a spare FOB with key secured on the bike to prevent stranding in case I were to get separated from my main FOB.
The first part of your problem with the "IMMOBILIZER ERROR" was not a issue with the stuck Kipass activation switch. If when you press in the key and the gauges sweep, the switch is ok. That's not to say that if the gauges do not sweep that it's the switch for sure, it may be or it may not be. But if the gauges do sweep, the switch is ok.
From what you're saying in the second part of your problem it sounds to me like when you had your bike programmed to 'see' the extra fob that you bought that the bike was not reprogrammed to 'see' the 'chip only' section of the larger fob. I think that your dealer screwed that part up.
See this attachment for more info. Look on page 3 and read the section on Key Fobs.