Agreed. This is simply a case of border control agents going overboard. I'm not defending it for a second (as a US visa holder, I despise the process I have to go through every time I enter the country) but these agents aren't technically inclined in any way.
When you arrive at their desk, they ask "what do you do for a living and what does your company do?". If you answer "The company makes chat software", you'd walk straight through. If you say "The company makes encrypted, secure chat software" then they are going to ask further questions. I wouldn't be surprised if they have a watchlist of words to listen out for, and "encryption" is one of them. Encryption is subject to export controls:
http://en.wikipedia.org/wiki/Export_of_cryptography_in_the_U...