Topic "Oil stains on floor after applying Polyurithane" a message from confused

I am so confused about oil stains that occured after I applied my first coat of polyurithane on my new floor.
Location: Bathroom. I had square marble tiles on the bathroom floor that were discolored (yellow) from many years and well water overflow. I placed a carpet over these tiles for many years.
I decided to install a "brown bag paper floor" http://www.youtube.com/watch?v=MvR2pfSdrmw
I filled in the cracks in the marble with spakling compound and let dry over night.
I applied an oil based polyurithane (PU) over the marble floor.
I placed my brown paper bag pieces with Elmer's Glue and water as directed and let dry overnight. (The floor was stunningly beautiful when dried). I was ecstatic because I couldn't afford a wood floor at the present.
I applied a coat of PU and when I was finished, I saw oil stains on parts of the floor.
After the floor dried, the stains were still there, so I had to apply more crushed pieces of brown paper to cover the oil blothches (or whatever those drips were).
WHAT HAPPENED? Did I not stir the can enough?
The room was warm and the heater vent was blowing on the floor, so it was not cold where this room was.
I'm afraid to apply another coat for fear of more drip stains. Can I apply water based PU over the oil based PU?
Please help!