I have this problem since just a few days. I've been a heavy Chrome user for several years, but it never happened before: Sometimes absolutely uncalled for pop-ups appear, when I click something absolutely legit. It seems to happen at a very precise rate of two pop-ups every hour or so. The pop-ups are not very varied, it seems to be a fixed set of some 4-5 ads.
At first I thought I caught some malware, but after a full scan with Malwarebytes Anti-Malware, I found absolutely nothing. In addition the problem exists only with Chrome. When I use Firefox, this never ever happens.
What is even more puzzling is that it happens on both of my rigs and started on the same day. I have a removable storage that I dock to both of them and access one machine from the other via RDP, but still...
(Just in case it matters: I run Chrome version 24.0.1312.57 m on Win 7.)