Project builders are run at the request of some build trigger. This might be resource changes (when you have build automatically enabled) or it could be the build action you're using: "build as Ant build". The build action may be inadvertently requesting a build of the whole workspace.
Put the following in a text file:
# Eclipse build
org.eclipse.core.resources/debug=true
org.eclipse.core.resources/build/interrupt=true
org.eclipse.core.resources/build/invoking=true
org.eclipse.core.resources/build/needbuild=true
#Managedbuild
org.eclipse.cdt.managedbuilder.core/debug/builder=true
org.eclipse.cdt.managedbuilder.core/debug=true
org.eclipse.cdt.managedbuilder.core/debug/pathEntryInit=false
org.eclipse.cdt.managedbuilder.core/debug/pathEntry=false
And run Eclipse with the additional switches:
-debug <trace_options>.file
This will echo trace prints to the shell in which you started Eclipse. You can use this to better target the bug report you'll no doubt file :)