I have sold a fair bit on Ebay and find that the item generally sells for a better price when I start it at 99p and with no reserve on it. It's my risk. It might not make its money, but it almost always does.
If I put a Reserve and/or a Buy-Now price on it, the set-up fee's are higher.
This doesn't mean that there is any funny business though. I know that Ebay is toss lately, for many reasons, but I don't think you have necessarily been the victim of any of that in this case.
Make sense??