You're not the first to notice this trend; actually, we had some discussion about it in the moderator chat room a few months ago. So I collected some data. Sampling which community ad is displayed on the home page at 10-minute intervals for a couple weeks shows that the distribution among different ads is roughly Gaussian, with no significant outliers.
(this omits the ad for the site's newsletter) The Physics Overflow ad was displayed more than average, but was certainly far from being the most common.
However, looking at the actual samples shows that the same community ad is displayed for a run of several hours. The exact length of the run changes according to some pattern I couldn't figure out (perhaps randomly), but the ad is not randomly chosen on each page view. I presume this is done to allow better caching. Anyway, I think this contributes to the impression that the PO ad was being displayed more than it should be. If you tend to notice one ad more than the others, then when you see it the first time, you're more likely to register it when you visit the page in the future. While that ad is the current one, then it is being displayed more often than it would be if the ads were randomly chosen at each page load, and your brain registers something fishy about that. On the other hand, during a run of any other ad, you don't notice it at all and your brain doesn't register the fact that you're going a long time without seeing the ad you focus on.