Thank you for contacting us with this information.
May I please clarify with you the next things so that we could find a reason for the issue and way to solve it?
Here they are:
1) First of all, I kindly ask you to check if this file has the same Code Coverage data (covered/uncovered lines and coloring) in Developers Console. The reason for my question is that we get all the code coverage directly from Salesforce and this would help us understand if the IDE doesn't handle the returned data properly.
2) Can you please tell me if you see that there are 3 uncovered lines in a file in the Code Coverage panel in the IDE or you get this value from your Organization?
3) Is this reproduced for one file or for some/all of your classes with uncovered lines?
Can you please check if you would see red lines in covering of your class when check covering by test methods - this option is available for you in the top right corner of the code editor in an opened class file.
Also, you can send us a bug report with the attached log files directly from the IDE so that we could analyze your TWS logs - the option for this in the menu Help -> Report a Bug.
Looking forward to hearong back from you.