Well, it sounds like the service tech at your shop failed to properly secure the tension on the cam chain when they removed the old CCT.
I do 95% of my own maintenance on my bike, but I do take it to a shop for the valve checks. I've been to four different Yamaha shops in the nine years I've owned the bike, and at each shop, the techs were not all that familiar with the Super Tenere. At one place, they'd never even seen one before. That doesn't mean the techs aren't competent to work on the bike; it just means that sometimes, they aren't totally familiar with the quirks that individual bikes might have. A tech might think, "hell, I've changed lots of CCT's on Yamahas, this won't be any different" and then doesn't look too closely at their service instructions to realize how critical it is to keep tension on the chain for this particular model through one method or another, or else the results are exactly what you experienced. Or maybe the tech used a wedge or something for tension, and knocked it loose while he was working on the bike. Mechanics do screw up sometimes, even when they're following the book.
I would think that, for an experienced tech, changing a CCT would be a pretty easy process, as long as they familiarized themselves with any quirks of the particular model they were working on before they started turning a wrench. I would get pissed though if they tried to charge me for the extra hours of correcting their own mistake. The only way the chain jumps when you change a cam chain tensioner is if you do it wrong, and that's on them.