I noticed that some Month ago. I've changed my Hardware and System in the meantime, but it still happens. (2.49b/2.5)
before: XP32; GForce
now: Win7 64; Radeon 4850
In all kind of animations in Blender GE, are some strange micro lags. I hope i explain it right. Shown best with linear animations. Please have a look at the file.
All Cubes have a different Way to move. Such micro delays have effect to all cubes.
EXE-Tests in XP32 does have the same Results. (Don't run in Win7 64, so i can't test.)
Maybe You can find something out.