Bad alignment will make the chain jump, thing is chains don't WANT to jump the sprockets. Their very design means they pull themselves onto the sprockets.
I have had chains that were absolutely worn to their limit, like 17000 miles (scotoiler) and it stayed on. Slack as a prossies chuff but stayed on.
Tight spots don't free off either, the tight spot is something that forms in a chain from use. Something to do with frequency, tension and power transfer effects on the chain. There will always be one and you having a big tight spot, big enough for the chain to jump says adjustment.
Unless your packing more weight than the average brit, (according to Yamaha that's about 80Kg) which will affect how you adjust your chain.I'd say the chain adjustment was done wrong at the replacement and now the chain is, well. Knackered really, wouldn't be the first time a garage has done a chain up a little tight so that its right when the owner checks it a few weeks later.