Open-rate is measured for HTML and multi-part messages only, AND if the "track open rate" box (under Tracking and Reporting) is checked for the messages you want to track.
If you are sending each message in different formats (HTML, plain text, and/or multi-part) and you have contacts that have PLAIN TEXT as their FORMAT PREFERENCE, then those contacts will not be counted even if they actually opened the message.
For a more accurate open-rate figure:
1. Make sure that all your messages are in multi-part or HTML format; AND
2. Make sure that the format preference of your contacts are either set to HTML or 'No preference'