Has any one ever used wax to waterproof a pertex garment the good old fashioned way you would wax cotton? Are there any good reasons not to? I have used wash in DWR treatments in the past and frankly they are pants.
No, cannot say I have ever even heard of doing that. Does not sound a good idea. Pertex's selling points are light weight, packability, tight windproof weave with a degree of breathability. Waxing will compromise all of those in the hope of increasing water resistance. My experience with Nikwax on single layer and thin double layer nylon and polyester is that it doesn't work all that well when there is already some commercial PFC type DWR on the fabric.
I would have doubts about how well cotton waxing wax would stay in such a tight, smooth and non-absorbent weave as Pertex. You could try it on a swatch.
Pertex was never really made as a waterproof fabric so, by attempting to wax it, you are trying to make it become something it isn't. I'd leave it alone and enjoy its performance as a lightweight, windproof fabric that 'breathes' pretty well and dries very quickly.