All of the licenses described in this book can be broken up into two parts. The first part asserts that the person granting the license, the licensor, has the right to license the work to which the license applies. This representation may be implicit or explicit, and may be limited to specific types of rights. A licensor may, for example, assert that he has only applicable rights under copyright to the licensed work and makes no representation about patent rights that may apply to it. The second part of every license is a grant (again, however limited) by the licensor to the licensee of rights to that licensed work.
Obviously, both parts of the license need to be there in order for the license to be effective. When the first part of the license is there and the licensor has all of the rights necessary to grant them to the licensee, the only question is the relationship between the licensor and the licensee under the terms of the license. However, significant complications arise when a third party has legitimate legal claims to the work purporting to be licensed.
In the case of copyrights, a creator of an original work (defined in the legal, not the artistic sense), can confidently license that work, at least to the extent to which it may be governed by copyright law. The creator (hopefully) knows that he or she has not plagiarized the work from another and therefore has the right to license it.
Patents, however, present more complicated issues. It is more difficult to obtain and retain a patent in the first place, and there is always a risk of possible, and possibly unknowing, infringement of a patented process by the licensor, and, accordingly, by his or her licensees.
Unlike copyright protection, which does not even require filing or a formal notice on the copyrighted work, obtaining a patent from the Office of Patent and Trademark requires filing of relatively complex and laborious paperwork, including, most importantly, some explanation of the novelty of the patent in question and how it differs from processes or mechanisms already known. This generally requires the participation of an experienced patent lawyer. But obtaining the patent is not even half the struggle. Because of the profitability of patent royalties, patent holders tend to be very jealous of their rights and patrol the boundaries of their patents vigorously, attempting through the courts to extend the boundaries of their patents as much as possible and at the same time to narrow the scope of patents held by others. This can be, as you may imagine, an extremely expensive and time-consuming ordeal.
Even if a patent holder has licensed that patent for use in open source software, they may not have the inclination or the resources to defend that patent. This may have substantially negative consequences for the licensees of that patent. Although the licensee may have, in good faith, undertaken the use of the licensor's patent in full compliance with the terms of the license, at some point in the future, that patent may be narrowed or eliminated through litigation by a rival patent holder. Because of the continuing use of that narrowed or eliminated patent, the licensee of the original patent may be liable to a competing patent holder for a claim of infringement. It is possible that such a licensee would want to take action to protect the licensor's patent, by initiating or participating in patent litigation in situations in which the licensor is unwilling or unable to defend the patent. This can, of course, get expensive.
A larger problem is that there may be patent claims that apply to the licensed software but are known to neither the licensor nor the licensee. Because licensors can only license works that belong to them, the existence of a particular software license is no protection for the licensee against claims of infringement that are not brought by the licensor but by a third-party patent holder. There are no easy solutions to this problem. Software patents are frequently granted and often maddeningly vague.
 For a more thorough discussion on the effects of patent laws and licensing on open source and free source software, and a compelling argument for limiting the application of patent law to software, see "The Danger Of Software Patents" in Free Software Free Society: Selected Essays of Richard M. Stallman (Free Software Foundation, 2002).