I'm not a running shoe fitter, so take my thoughts with a pinch of salt. But...
If your old shoes were support shoes for over pronation, you may have been running slightly flat footed without realising it, as the shoe would correct this. In your new shoes, you're continuing to run the same way, but as the shoes don't offer the same support, you're now aware of the flat-footedness. Gait analysis shows how you run for a few minutes when you're fresh, not how you run after a couple of hours when you're tired and your legs are all over the place. So for a quick try-out the shoes feel fine, but on longer runs they don't, as you get more tired and start slapping your feet down...
If the gait analysis was done correctly, my assumption would be that the shoes are okay for you but will feel odd for a while as they don't have the (un-needed) support that you're used to having. Perhaps wear them just on shorter runs for a few weeks, to start utilising the muscles in your feet which can now work in place of the support in the old shoes.
It might be a bit like when people change from cushioned running shoes to 'barefoot' style shoes - they can't just put them on and keep running the same distances they've been doing previously. They have to start off with just walks then short jogs to gradually accustom their feet to a new way of running.
And after all that rambling, I'd also add that there is also the chance that the shoes are just wrong for you! 
