Invalid patents remain unchallenged
For various reasons, when software patents are considered to be invalid, they're often not proposed for re-examination.
 Case #1: Buying a licence is cheaper
One example is the Divine e-commerce patents. The patent holder asked each "violator" to pay less than a challenge would cost.
This problem is also explained by patent attorney Dan Ravicher:
"...the remedies, what happen when you infringe a patent, are critical to think about when you talk about these issues of patent policy. So, most software technologists think the penalty for infringing a software patent is too high. And even if they're not found guilty, the risk of being found guilty one day causes them to either chill their behaviour now or divert funds to build a "rainy day" fund to protect themselves, etc. There are also the litigation abuses, primarily from these non-producing entities. The cost of litigation is so high that patent trolls know, if they offer you a licence for $200,000, you're going to take that every single time, just like Chris said. The cost of defending yourself in a litigation is so much more than what they're offering you a licence at, that even if you think the patent is worthless, it's still economically wise to pay them a licence fee rather than take it to court."
Similar is also described by venture capitalist Fred Wilson:
When that entrepreneur and the company he/she creates is hit with a baseless claim from a patent troll represented by lawyers working completely on contingency, it's a very big problem. As you can see, it can take a lot of time and money to fight and win.
The other option, and I see our companies do this all the time, is to pay a fraction of that $500k or more to settle the case and make the patent troll go away. That can be $25k to $100k in my experience. But that payment just funds the patent troll to go do it again and again.
 Case #2: There are just too many
- Sun Microsystems inc.#Paying IBM for nothing - Sun didn't infringe the named patents, but paid IBM because IBM had thousands of others
- MPEG video formats - with over 1,000 patents covering these formats, who would bother invalidating one?
 Case #3: Not my problem
- Black Duck's licence compatibility patent - which could, but won't, be invalidated by Bradley Kuhn
 Case #4: Cost too high, outcome uncertain
 Related pages on en.swpat.org
- Costs of defending are astronomical for developers and SMEs
- Invalidate patents based on subject matter
- Cost of defending yourself against patent litigation (Related because the unchallenged, invalid patents can then be used against developers who can't afford to challenge them)
- http://www.pubpat.org/assets/files/ftisapresentation/RavicherFTISAPresentation.mp3 (time:30:30)
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