Open-rate is measured for HTML and multi-part messages only AND if the Track open rate for HTML and multi-part messages box (under Tracking and reporting) is checked for the messages you want to track.
If you are sending each message in different formats (plain text, HTML, and/or multi-part) based on your contact's format preference, those who opted to get them in plain text will not be counted even if they actually opened the messages.
For a more accurate open-rate figure, always set the format of your messages to HTML or multi-part.
If you will be setting the format of the messages to Contact's format preference, then make sure that:
1. The format preference of your contacts is either set to HTML or No preference
2. The Format to send when contact has no preference setting is set to HTML or multi-part