HDR Bracketing and Intervalometer - Shifted Photos

[Sanfu]

Hi,
I was shooting a (2-frames) HDR timelapse with my 60D and something really strange happened. I'd never had such a problem before. I don't know if I can explain it properly. Every shot was a little shifted but every other was not. I mean, all the darker exposures were a little shifted compared to the lighter ones. This does not happen when I use HDR Bracketing without Intervalometer nor Intervalometer without HDR. Of course I can align them in SNS-HDR but this somehow resizes the final HDRs, so every frame has a different resolution. Could you help me please?

Thank you