tedster - 3:07 am on May 14, 2012 (gmt 0)
It does sound like a tangle - and no, short of some message in WMT I can't offer a definitive way to tell which of these factors is active for you. A little more time should sort things out a bit more for you.
You should verify the technical transition to a new URL structure no matter what (301s as appropriate, with no internal lnks going through a 301.) And definitely watch out for what the third party SEO company is actually doing to generate 1-way links, too.