Thank you for your bug report.
May I please clarify with you the next questions so that we could find the exact reason for the issue?
Here they are:
1) Is the issue reproduced after you save a SOQL query file?
2) Is the message that you get a warning or an error?
3) Do you get results after executing your SOQL query in the SOQL query builder? If no, does a header of the table appear in the results section?
If the issue is reproduced after you save your SOQL query, please send us a bug report directly from the IDE - you can find the option for this in the menu Help -> Report a Bug, please enable the 'Attach Log File' checkbox and out your email.
All this information will help us greatly to solve the issue.