I have a similar problem but it doesn't stop me from being a good programmer. What it means for me is that when I sit down to work on a large project, it can take me a while to get up to speed with it as I reload/reaquire the knowledge. And I think that's totally normal.

In your case it might mean that your memory isn't "flaky," but rather that the way you perceive the content of a program is high-bandwidth, which would imply deeper understanding of the content even though such perception has the side effect of making your memory seem worse.

Still, you should check with a doctor on whether you might have some weird anemia or something.