Nice to see the encode is running :-) I sometimes get greatly differing encoding time for the same video as well and I don't know why either. It slowing down gradually is pretty normal too. The second pass of my test encode ran at 1FPS average while the first was almost exactly as fast as on your end.

If you want to work with your computer while it encodes just use the task manager and change the priority of x264.exe to either "Lower than normal" or "Low". I advise against doing CPU heavy stuff, but for the rest it should be ok.