You might be right. The second file saved has an A in front of its name. That is, if one is titled "Test", the second file will be called "A_Test". I assume the A is for Alpha, and I think C4D keeps wanting to make a Separate Alpha, even though I don't tick "Separate Alpha" as an option. I think it's a bug. In fact, I can't even select "Separate Alpha" in the options. It's permanently grayed out. C4d insists on giving it to me whether I want it or not.
No I don't see it rendering twice, and, yes, I can just delete it, so not a huge issue, just a nuisance.