In 2003-2006, we built a service that was a financial system to exchange financial data through various means including AS/2 EDI over HTTP with big companies and the government suppliers such as AAFES (Army and Air Force Exchange). Initially we had RSA, PGP and a custom encryption in there, the latter two for other features besides EDI. We got a letter from the FBI asking us to switch only to RSA, they wanted to know about our use of PGP and wanted to see our custom encryption if we continued to use it. Being a small/medium company we switched to just RSA to avoid any issues. It was an odd day, when I came into the office they told me I had an FBI letter on my desk and you can imagine what happens around an office when something like that happens. Very strange day indeed.
Moral of the story, if you create your own crypto or aren't using the ones you are supposed to use, in any capacity, expect some knocking.