The owners manual says only use the switch to warm the engine when cold (like in the morning). You should not use that switch to try to get the bike to stay on after you have already been riding or come back to the bike after it's been parked. That's when your idle needs adjustment so that it idles around 1300 rpm all the time.
The idle lever on the 696 should be turned on at every startup, get use to it. There are definitely other factors that will cause the low idle like the charcoal filter being removed as one. My 696 had many of the same issues but they were sorted out.