There are several things that can cause this. The most popular one is that you have two different projects that are trying to access the same PDB file. The reason you are only seeing this with IncrediBuild is because with IncrediBuild many of your projects are being executed in parallel (when in standalone the projects are executed sequentially). Detect the project that fail and verify whether you have another project that executes in parallel to this one and direct it's PDB to another PDB file. If this is not the case, let me know, there are other less common scenarios.
(Disclaimer: I'm an IncrediBuild employee)