"You shut down your computer because of a problem"

Every time I boot my 2011 Mac Mini (Marvericks) I go through the rigmarole of being told I shut the computer down because of a problem. But I didn't. In fact it's behaving faultlessly apart from this one little niggle. I've repaired the disk permissions, verified the disc. It shuts-down quickly with no issues.

I even tried clearing the PRAM, but despite following what I thought were clear instructions by holding down Opt+Cmd+P+R at switch-on, all I got was the spinning-globe telling me it was downloading the OS from the internet. (I held the Power button in at that point to close it down, so at least next when it booted and told me I'd shut the computer down because of a problem, it was correct for once!) I've even tried leaving it unplugged for a while to clear-out the SMC. No avail.

Sometimes it's the littlest things that do your head in. Any ideas?