Microsoft just responded to our request for comment with this statement:
Xbox LIVE Arcade has long been known as the premier destination for digitally distributed original and classic games - making it a very appealing platform for game developers. We don't disclose details on our business contracts, but what we can tell you is that we work closely with all of our partners to provide the Xbox 360 community with the best entertainment possible while making publishing a title on XBLA an attractive prospect.
While not really a confirmation nor a denial, it does sound as if they are reacting to what our multiple indie developer sources told us was fact. We will be meeting with some of the XBLA indie development folks with Microsoft later today and will make sure to follow up with them about this issue.
Microsoft Cuts Indie Royalties in Half [Kotaku AU]