No such problems with phoronix, here, but then again, I couldn't legally install the proprietary flash if I wanted to (and generally don't bother with the freedomware gnash/lightspark alternatives), as I can't agree to the rights and black-box-liability waivers and thus in the US at least, probably would be held not to have the legal right to install and use them, even if I did want to use blackbox proprietaryware I can't examine from folks already demonstrated not to respect the user's rights, even to examine the code he's expected to agree to waive liability claims on! The noscript and requestpolicy extensions help tremendously as well, and I have privoxy installed with a phoronix-specific blocker for that page obscuring blocker ad that lacks a working close method if scripting is disabled.
But I suspect the biggest phoronix audience is gamers and others that have no ethical or legal problems with proprietaryware, and the flash ads you mention probably work for many of them. Meanwhile, it's quite unlikely I'd be in the market for anything advertised anyway (especially on a site using abusive tactics such as page-blocker ads with no way to kill them if scripting is off), so even if it's per-view paid, it's ultimately better that the advertisers don't get that view from me since that only brings down the response rate and therefore ultimately the per-view fees they're willing to pay.
And life is /so/ much better without the incessant ads... the reason I gave up on TV and radio years ago, for computers and the net, where I could better control such things. (One thing I've noticed, tho, I can listen to internet radio in German or French or Italian or Japanese or Korean or... or even local AZ over-the-air Spanish stations, and have a higher ad tolerance, since I don't understand them and thus they aren't such an insult to my intelligence after I hear them the 10th or 100th time. It takes to the 100th or 1000th time if I can't understand what they're saying anyway, before the invariant recorded repetition itself gets to me.)