my wife and I crossed at Nogales on the 11th of June 2011.
Had some issues getting the bikes into the country (guess we bumped into the wrong guy at Banjercito, that seemed to be the problem) When we tried again, there was no issue at all.
We felt 100% safe here, and we are still in Mexico now. (ner Perto Vallarta).
Great country, great people and good food...
Also military checkpoints have not been a problem.
One time the police pulled us over (with sirens, lights etc, and yelling thourh his speaker on the roof). Gave us the shivers, but he wanted to help us (we were driving around to look for a hotel, which he figured out so he pulled us over to help us finding a hotel). When I asked him why he had to pull me over this way he simply answered: 'well, I had to get your attention... !'.
Just go there, and have fun! Perhaps we can cross Darien together? We plan to be there end of September, first week of Oktober.
just contact me on www.farawayfromflakkee.nl