I don't have any explanation for this in that case, only to say that I've noticed a few intermittent anomalies with mine that don't occur all the time.
I'm still convinced there's an issue with my software in certain situations, so maybe a re-install might help, but I'm guessing you'll've tried this already.
Sorry, that wasn't at all helpful.
Edit: Unless you've got some clash in controls settings in game? Is it possible that there might be a conflict of controls somewhere if a control function is mapped to two control axes/buttons or vice versa? Also, have you tried the same situation in other sims? If it's ok in IL2 for instance but not in CoD, you'll know the prob is in the control settings in CoD. The 'ok in windows' would also point to this. Sorry if this sounds patronising but the keys and axes control settings can conflict sometimes!