Hi,
You should check if the project builder is executed and on which targets. By default, the default target is set to run After a “Clean” and Manual Build. So whenever you do a ‘Clean’ on your project, the project builder will run by default.
Right click on the project > Properties > Builders. Edit the ANT Builder you have created. Switch to ‘Targets’ tab. If the default target is selected for ‘ After a ‘Clean’ ‘ and ‘During a clean’ , click on ‘Set Targets’ and turnoff the selection.
Here is the screenshot for your reference :
For a clear understanding on when the targets will be executed, please check the ‘Project Builder Ant Targets’ topic under ‘Ant buildfiles as project builders’ here : http://help.eclipse.org/juno/index.jsp?topic=%2Forg.eclipse.platform.doc.user%2FgettingStarted%2Fqs-81_basics.htm
Let us know how it works for you.