Hate to say it, but the new program has many more glitches than the old one. So many important cards don't work properly.
To be fair, the "old one" had over 6 months of bug fixes by the point at which it had been shut down. Many of these bugs were found by the community. You guys have had the new version of the game for 15 hours.
I can tell you that it's VASTLY easier for the developer to make fixes in the new client than it was in the old client. After the Trainer Challenge was relaunched, the rapid pace at which bugs were fixed was pretty stunning, after having suffered through Eviolite, Rocky Helmet and Victini bugs for months in the old version.
The reason we're in open beta is so that the community can help point out these bugs. I'd encourage everyone that encounters a bug to follow the procedure outlined in this thread. The forum moderators collect that feedback and send it to the development team on a regular basis and bug fixes are deployed in regular patches (yet another advantage of the downloadable client).