So how I fixed this. I've edited the targets file of SlowCheetah
This can be found C:\Users\BuildUser\AppData\Local\Microsoft\MSBuild\SlowCheetah\v1 On your build server. Open the file and locate the following lines:
<BuildDependsOn Condition=" '$(IsWap)'!='true' ">
<BuildDependsOn>
$(BuildDependsOn);
TransformAllFiles
</BuildDependsOn>
And i've removed the condition.
Result:
<BuildDependsOn>
$(BuildDependsOn);
TransformAllFiles
</BuildDependsOn>