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OmniFocus doesn't make any decision about whether to use a proxy server or not, unfortunately: OmniFocus connects to its sync server by asking the operating system to connect to the sync server's URL, and the operating system decides whether that URL needs to go through a proxy server or not. (So if the behavior changed recently, it seems most likely that it was caused by an update to the operating system or to the proxy configuration.)

I'm not sure what the rules are for manual proxy configurations (maybe everything goes through the proxy, including LAN traffic?), but if you use an automatic proxy configuration you could presumably solve this by adding an appropriate exclusion rule to the proxy auto-config (.pac) file, so it wouldn't send traffic intended for your local LAN through your Internet proxy server.

Hope this helps!