Frustrating for sure, but the terms and conditions of BWR does state rates 20% below rack rate (or manager negotiated rates) will not be eligible for points/miles.
I do know some hotels within the chain will go 'above and beyond', giving you those points, but please do keep in mind that each hotel is independently owed (as opposed to the large chains). Your experience will vary between properties for that exact reason.
As for the 'corporate' policy with BW (the parent company), I completely agree it is ridiculous. I am an independent contractor and based on where I live BW is really the only chain that is a viable option for points earning, when I contacted them regarding acquiring a corporate discount I was told my company would need to spend 500 nights PER YEAR at BW properties. Ha, as I am only one person this was entirely impossible! I would have figured BW would be geared more toward "the little guy" as the Sheratons and Hiltons of the world get a large share of the business pie, but it appears that is not the case.
That is not to say all BW are awful, some are a great option, you just have to be clear in your negotiations what you are expecting to get from them.