I'm the other person that had this issue, and as Brad pointed out, it's almost certainly due to sharing a document directory between installations. To resolve the issue I uninstalled BeerSmith 2.0, moved the documents directory out of the way (renamed it to <directory-name>.bak), and reinstalled BeerSmith 2.0. Then I verified that the sample recipes showed their ingredients. Assuming they did, I then imported from the renamed documents directory. This is VERY important because somewhere in that directory is the configuration file(s) that became corrupted! I believe this is why uninstalling and reinstalling didn't work for you. If you have equipment, water profiles, etc., you'll need to import those as well. Easiest way I've found to do that is to open the file and then copy/paste from the opened file into BeerSmith's own corresponding location. Let me know if this doesn't resolve the issue for you and I can help you troubleshoot it a bit more.
Brad, given that BeerSmith features a user-assignable documents directory, and given that the main reason folks would want to do that is to allow some form of sharing, you probably either need to issue a warning when changing that setting that using a shared directory can cause issues or you need to come up with some kind of exclusive lock file mechanism that prevents multiple running instances from writing to the shared directory. It seems to me that multiple readers are fine, but you should allow only a single writer at any given time. Of course, then you get into stale lock management if BeerSmith dies while holding the write lock, etc., but I imagine this won't be the last time you see this hard-to-grok problem.