If the site is down for few minutes and you refresh the cookbook, the application will exit whiteout any error message. Moreover, if the server is still down, you cannot start it again.
Short solve: Verify in advance, if the server is working :)
As any recipe modification needs refresh, this bug is annoying (or you have to work manually until the recipe works well).
I just tried ping -t fold.it from a Windows command prompt, and saw a big block of Request timed out responses. Then a series of Reply from 128.95.160.161: bytes=32 time=52ms TTL=48 responses, then back to Request timed out. It not clear if the website timeouts are affecting the Foldit client. Previously, I don't think the client would "block" waiting for network responses.
The client is blocked if you ask for a cookbook refresh, otherwise is not affected. Affected at start also.