Unfortunately, while the capture process is pretty good, it's not perfect. So it may not capture everything perfectly or even understand what it is capturing in some cases. To be honest, I'm surprised it works as well as it does!
However, this doesn't really address your issue. I'm at a bit of a loss here trying to understand exactly what is happening. I'm wondering if seeing it first hand would assist in sorting the issue. If you can, try using either screenr or jing to record the process where it is failing so that we can see. Then post the link here for us to examine.
Helpful and Handy Links
Was wondering if it is not due to the used keyboard? I'm using AZERTY - Belgian version, have to translate quite a lot of shortcuts such as CTRL-0/1/2/3 for zooming becomes CTRL-à&é".