From a commit where we mark a WebKit test as "always expected to fail":
Safari has a unique handling of the BOM characters among browsers. There is a strong suspicion that this is a security problem, so we follow the rest of the browsers on this one.
There are a few places we diverge from WebKit/Safari in terms of web compatibility; the big one is v8 but there are also many differences at the networking layer since Safari relies on the closed-source Mac networking layer. This includes cookie handling and mime sniffing aside from the obvious HTTP protocol bits.
We've been bitten by a variety of bugs in the Windows-native HTTP library we used, including stuff like missing HTTP 0.9 support and even bluescreens(!) so now we've switched a network stack of our own (It's not currently in any of the Google Chrome channels, though). It likely has a whole new set of bugs, but at least those are bugs we can fix.