Not sure if this was touched upon since I knew a few people were talking about this before without anything conclusive, but I think there's definitely something up with the Ys Chronicles currently on the store. I previously bought it last year but I never got around to it and totally forgot I even had it, and to get ready for the Vita I wanted to pick it up. For some reason the store allowed me to re-buy it, which isn't usually supposed to happen. Then when I was on my download list I noticed the old one, realized what happened and sent an email that is still waiting a reply from Sony (hoping for a refund).
Anyways, the older version of Ys Chronicles was able to be loaded on my Vita, but the newer one that I just rebought wasn't. It looks like they did something to the game and re-released it that is causing it to not be compatible, but the filesizes of both versions seem to be the same.