Depending on your last update, the 'too long to encode' warning-message was added only recently; you may have been skipping frames for quite a while, and only just have been warned about it now that OBS pops up a warning when it happens (it didn't before).
Also, you're using Monitor Capture mode. That should be a last-resort ONLY under Win7. Should instead be using Game Capture, or Window Capture with Aero ON (so OBS can grab the window texture from the offscreen Aero buffers, much faster performance).
I'd also recommend checking on your CPU utilization, stepping, and temperatures; it's possible that over time dust accumulation may be making it overheat and down-clock itself for safety... 720p@60fps is right on the edge of what an i5 can handle encoding, even with a low-CPU utilization game. You may have pushed over that edge, if that's the case.
Also, on a side note, Twitch's standardization measures require the use of CBR, not VBR. You should enable it. Also appears that your network connection may be having problems with the delayed sends evident, as well as the dropped frames.