Cristina, the "open" is registered by Marketo when a hidden image (probably a 1x1 clear png) is retrieved. This can only happen if the email is opened and images are displayed. When you are doing your internal testing are you opening the email and displaying images? Many email programs (Outlook and Gmail for example) block images by default, requiring you to click a "display/show images" button. Users who don't click that button will not be registered as opening the message, creating a false negative.
On the flip side, many users will turn on displaying images but will also use the preview pane in Outlook. This can create false positives where it shows the user opened the email when in fact they didn't really.
This is not a problem unique to Marketo and therefore email opens should always be taken with a grain of salt.
Having said all that, Marketo really should retroactively mark the open if a user clicks a link (since that obviously means they openeed it). I would have expected this to be the case, but it sounds like maybe not.
Hope that helps.