Although I know nothing about European patent law and almost nothing about US law, here is the relevant US code:
"Except as otherwise provided in this title, whoever without authority makes, uses, offers to sell, or sells any patented invention, within the United States or imports into the United States any patented invention during the term of the patent therefor, infringes the patent," (emphasis added). [1].
It seems to me the issue would be whether writing the code for patented software constitutes "making" it. Who knows. The patent system is such a joke.
[1] http://www.law.cornell.edu/uscode/usc_sec_35_00000271----000...