given that retroviruses are sloppy, basically any any all genes have at some time been reverse transcribed.

True, but that's a tenuous argument. You can't prove that a particular gene has been reverse transcribed and that its cDNA is therefore a naturally-occurring product, unless that cDNA is essential to the virus' life cycle. To invalidate the patent, you would probably have to actually observe the natural reverse transcription of the complete sequence.

In any case, the original point I was trying to make was that the natural occurrence of the mRNA does not make the cDNA a naturally occurring product.