e.g. with 0.9c I was pleasantly surprised to see the poolside reject rate fall to a new all-time low of 0.38%. After switching to 0.9d, its gone up to 5.27% and climbing, and I can see reports of rejects locally a few times every minute. So I've gone back to 0.9c for now. Rejects such as:
"DEBUG: reject reason: unknown-work"
"DEBUG: reject reason: high hash"
Rowan, I had the same issue, except mine was about 25% rejected. I was running on a Raspberry Pi. I updated to the latest firmware and made sure everything else was up to date, recompiled newest cpuminer with the config commands Mr Jinx suggested, and now it seems to be back to normal.
I imagine mine was 25% ish rejects too, from the amount of locally shown errors, but it takes my pool stats ages to update, so I just saw it getting worse and worse. I'm using windows 8.0 but thanks for the suggestion. I've gone back to 0.9c for the time being.