I don't post here much (more to read than I can cover) but anyway....
First, I think they don't make Masonite any more--that's a brand name--but there are several companies that make compressed hardboard that is similar to it. Unfortunately, there seems to be a very wide variation in how hard the hardboard actually is.
Next, it's not clear to me if you're using traditional gesso or acrylic primer that's sold under that name. My guess is you're using the acrylic stuff. Real gesso is made with whiting and glue (traditionally rabbit skin glue or today sometimes other kinds) and is often made by mixing various proportions of the powdered ingredients in water. Acrylic "gesso" is dilutable in water, too, of course, and in my experience, the water soaks into the hardboard and will bring up the brown stains you've seen. On the other hand, real gesso hasn't done that for me, probably because of the glue. Some experts recommend that you give the panel a drink of diluted glue solution before applying traditional gesso. I'd guess that's why traditional gesso doesn't bring up the brown stains.
Sanding the smooth side of the hardboard is actually a good idea when priming it because it increases the mechanical bonding of the primer to the wood--I use 120 grit paper. It doesn't require a great deal of sanding, btw--barely enough to rough up the surface. You don't have to do it, but when using traditional gesso, sanding is a good idea. Most who prepare their own gessoed panels sand between coats as well, and may apply as many as six coats (usually at least three).
I don't know if this is helpful or not, so if not, then "never mind."
Oh, and if you don't want to go to the trouble of doing it yourself, you can get some lovely prepared panels from
http://www.realgesso.com/
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