Marketpress new upgrade creating "store-2" permalinks and problems with mp_product.php

Having more trouble with the upgrade. Noticing that on the upgrade some more issues:

1. Customized page templates that were previously working...are no longer recognized in the template. If there is a mp page template, ie:

mp_product.php

the product page doesn't show a buy button or image..its un-usable. If I remove the file, it shows a product page

2. Permalinks
the store used to reside at:

http://thedomain.com/store/

however now it appears to reside at:

http://thedomain.com/store-2/

However the linking to http://thedomain.com/store/ at many locations

Anyways...looks like this plugin was perhaps not tested in a multi-network set up? Really excited about all the new features, but there are serious issues that have made the site un-usable and would really appreciate some help! I ready to work with the developer and have support access open.

Thanks!