Indeed they are. The summary is a bit misleading, in that it suggests that the EFF is asking the USPTO to actually look for prior art. The real request is actually a request to develop a system to make searches for prior art actually turn up useful results.
Prior art is a difficult thing to research, because you're often searching for evidence that someone before the filing claimant thought of a similar idea and considered it just not worth filing a patent on. You're looking for industry periodicals, journals, doctoral theses. In the case of software patents, you can expand that search to textbooks that use the claimed code (or similar) as an example. For the really low-level things that people try to patent, even general mathematics textbooks (under the theory that nothing is more obvious than copying an equation out of a book). Rather than develop a corpus of searchable prior art -- and assuming that Congress doesn't have a sudden epiphany on software patents -- it makes more sense to increase the ability (read: decrease the cost and effort) to challenge a patent on prior art grounds at every steps of the process, and even after a patent is issued.
The examiners know what they're doing. However, the lack the time for in-depth searches for every such claim, or equivalently, the department lacks the funds to hire more people. The government has taken neither of the steps that would help alleviate the problem: pay for more examiners, or wipe away large swaths of new patentable IP (software patents) that are consuming most of the time. The EFF advocates for the latter, but probably won't be able to get it due to the complications of trade agreements.
You see, the U.S. has done a magnificent job crafting trade agreements which bind its own hands. Most of these agreements, such as NAFTA, are crafted to account for what happens when a government no longer wants to "play fair" and tries to tax some business, nationalize some industry, or invalidate some class intellectual property by re-classifying it. How do you have legal protections when government lawmakers are the violators? To start, you create an international system of extra-governmental courts that's beholden to no one that can dole out fines which other member governments can collect directly as tariffs. Then you make a whole slew of things trade violations, including the creation of new classes of "lesser" IP, or the destruction of whole classes of existing IP. Which when you get down to it, is exactly what the EFF proposes. Even if the U.S. realizes it would be a good idea to remove or alter software patent protections, it can't without violating its own trade agreements.