Have you recently made any changes to an affiliate program or banner ads campaign?
An extra 100,000 links is actually pretty easy to come by - it could be one site with dynamically generated pages linking to you. I wouldn't be too worried about this but you may want to look into it for your own peace of mind.
With regard to your linking root domains dropping - do you have any records that show what type of sites have been removed? It could be that you had a lot of directory links which Google has removed from the index. If this drop in LRDs hasn't already led to a drop in rankings then, again, I wouldn't worry about it but you may want to look into it further for your own peace of mind.