When I made the switch, I did everything by the book (my background is in SEO) including properly 301 redirecting the .us to the .com and alerting Google in Webmaster Tools.
The site completely disappeared from the Google search results--same symptoms as yours, with site: returning valid info but the site not showing up in search queries at all for the site's name.
This went on for 3 weeks.
Finally, after 22 days, it came back up in the rankings. Where previously it had been #4 for its keyword, it came back at #1.
No explanation from Google or in Webmaster Tools.
(If I may do a brief plug--our rank tracker will help you see if your site is ranking somewhere lower than the first few pages now, and will send you daily email updates so you'll know right away when you come back: http://whooshtraffic.com/rank-tracker/ )
Anyway, I'd have to say that this is par for the course for Google. It will likely come back in a few days or weeks. Time to play the waiting game, and develop some good links from your blog to your main site!
That is EXACTLY what is supossed to happen. Google runs a SE with over 5 billion URLs - if anyone tells you, or told you, that a transition was seemless and instantaneous, they lied.
To explain why, Google has this flow:
1. Crawl the old site - once it finds 301 redirects, it kills the old site and has no data on the new site yet.
2. Google crawls the new site, and starts to apply the old sites criteria - this is NOT, repeat NOT instantaneous.
3. All the "pre processed" signals are applied from the old to the new site.
22 days is a pretty short time to see things come back better, and I'd thank my lucky stars!