I have made my own copy of the linker in the project directory and changed the project to use that Linker and never had a problem, maybe try that.
Copy the intial file, move it to you project directory, then, I put all mine in a folder called LCF, go to project properties and change the following
C/C++ Build > Settings > Tool Settings > (Cold Fiire Linker) > Linker Command File (.lcf)
change this to
${ProjDirPath}\LCF\MyLinkFile.lcf
Obviously make this match your setup
