Yes, I've noticed it too. Even when you first insert a disc in the drive and the drive link blinks while it is trying to recognise the disc - both lights will blink. I don't see why there is anything wrong with it. I suspect that the logic behind the HDD LED is that it blinks when a UDMA4 (or faster) device is accessed. The manufacturers don't know which channel a HD is attached to (primary or secondary) so my guess is they assumed only HDs are UDMA4 devices and configured the LED to work that way. I might be completely wrong, of course.
In any case, the strange light blinking doesn't affect the performance of the computer or the drive, so I don't see it as a problem.