I got docked -2 for two down-votes I did in meta. Is this by-design? I thought that meta activity was divorced from rep score (I don't care much about rep, let alone two points of it, but I'd like to know).
At least in the meta-faq it says "Votes here do not affect your reputation in any way", and "Reputation here is entirely derived from the parent website", so this should indeed not happen!
The recent profile and reputation calculation redesign allows us to track reputation changes quite precisely. I checked your reputation history up to the date when you posted this question and the only negative reputation was from two downvotes to posts of yours gained on the main site:
Hence I assume this was some kind of a misunderstanding, rendering this question status-norepro.
Meta keeps track of reputation changes, as seen on, say your Recent reputation report from 1st Sep to today at (substitution your user id number for $YOURUSERID):
but this earned reputation has nothing to do with your effective reputation, shown on the top line and which determines your privileges here: that is, as TH. says, just copied from the parent site — although it is not quite identical, as you will often see a small time lag for earned reputation at the parent site to ripple through to here.
So, although it is peculiar to see a -2 reputation on the Recent report when there is supposed to be no penalty for downvotes, there actually is no penalty to your effective reputation, so this is all [status-bydesign].