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Experiencing this also, and sent an email to the ninjas describing my problem:
Ever since updating to the latest OmniFocus for iPhone, I am no longer able
to sync to my WebDav server. The message that comes up is:

Unable to synchronize with database with server
The certificate for this server is invalid. You might be connecting to a
server that is pretending to be which could put your
confidential information at risk. Would you like to connect to the server
The options under that are 'cancel' and 'retry'. Upon clicking either
button, omnifocus crashes. If I don't click anything, OmniFocus crashes. I
tried navigating to my WebDav server in Safari, and accepting the cert
there, but that doesn't seem to help.