There is a Cre8asite Forums discussion on having two sites on the same niche topic, residing on the same server, with the two domains resolving to the same IP address. Let me quote EGOL on this;
This is based upon observations of just a small number of sites. However, I am thinking that if you have two powerful sites competing for the same KWs and under the same ownership that google might show only one of them at a time. The sites I see in my SERPs that fit this will alternate in and out of the SERPs for the same KW one in and one out, occasionally both showing.
Backing EGOL up is the Site Admin at Cre8asite, Ron Carnell, who says;
I agree, Egol, and believe it's been that way for at least two years. However, to fine-tune that thought, I don't think it's so much the same keywords as it is the same "solution" (theme might be a more recognized word, but is still too broad). Naturally, keywords and theme often converge, but sometimes they don't, so it's a useful distinction (and may account for some of the exceptions you've seen?).
Some more good and even cute advice in the thread.
Forum discussion at Cre8asite Forums.