Literally as I started making this question it changed to what it should be, but I'm still curious as to why it was the case:
I had two tabs in Chrome open, one on meta and the other on rpg.stackexchange, and the rpg one (which I had been using) had higher rep. Confused, I closed the meta tab (which had been sitting idle for an hour or so) and in the fresher rpg one, switched over to meta. My rep was still different. I closed the browser and opened one tab in each again - still different. All of this in the space of about 2 minutes, but there was 20 rep difference, which I don't think happened as quickly in this case.
Why would my rep read differently in the different parts of the site?