I don't think the argument about software patents is related to capital.
The argument for patents is that it encourages people to invent things, because they have a guarantee of exclusive use which makes it easier to make money from their invention. It also encourages people to make inventions public instead of keeping things secret and then the knowledge being lost, since that's required as part of obtaining a patent. The US Constitution spells this out explicitly: the purpose of patents and other such things is "To promote the progress of science and useful arts...."
The arguments against software patents are basically that it doesn't have the desired effect. Much of what gets patented gets rediscovered independently, and thus it doesn't seem to actually encourage innovation. Nobody seems to ever go digging through patent archives looking for useful software techniques, so the fact of making patented inventions public also doesn't help.
None of this has much to do with software as capital, which would work much the same with or without software patents.