...have around 50 link 'partners' with 1000+ 'natural' inbound links...
I'm not quite sure how to interpret this, so I can't say how significant it is.
Do you mean... a) that you have 50 link partners, who account for 1000+ of your inbounds? b) or that you have 1000+ inbounds, and that 50 or so of them come from link partners?
Depending on how many other inbound links you have that are actually natural, I'd be concerned if the answer were (a)... ie, the bulk of your links from 50 partners. If the answer is (b), there's likely no worry on the link manipulation front.
You don't comment about whether your drops correspond to the Panda dates. That would be helpful information for the discussion.