Not sure what has happened there as its hard to diagnose without a URL to see if you have any direct issues.
I was going to say put the site back as it was if you were ranking before, but you have and still have a problem, from experience i can say 301's are not fast these days, i hear some people get indexed without any loss of rankings after a 301 but more and more people are losing rankings for whatever reasons, im 9 weeks into site change pretty similar to yourself and still Google has not passed the Juice from the old site to the new even though the 301 went really smoothly and all the new pages are indexed (they are just not ranking)
I would put the site back as intended I.E with the new redirects in place and go to the Google product forums where you can place your URL and hopefully people can get to see if you have an issue, there are some knowledgable people out there and also some idiots so research any advice given
The things you can check for yourself are
Make sure the 301 is correct and doing exactly what it should be doing, it may be worth posting your htaccess or php script in the relevant part of this site as there are a few who can tell you if you have any issues there [webmasterworld.com ]
also check the header responses and make sure you get either a 200 response or 301 redirected for the correct pages (Google for some reason picked up the non www version of my site for 2 weeks even though it was impossible to access that so some strange things are going on there
The last thing you want to do is confuse Google by adding and removing 301's confirm your changes and stick to them it may just be time Google needs