We had some tedious problems with our latest build not working and it turned out the hintpath for an assembly reference was missing in the project file.
It appears that ReSharper will not add the hintpath if it adds the actual reference. We had a reference to an assembly X that in turn had a reference to another assemby Y which was not referenced in the main project. ReSharper suggested adding the Y reference and we let i do that by using the Alt+Enter option. No hintpath was added to the project file. If we add the Y reference manually the hintpath is there.
This problem is described in detail in a YouTrack post that doesn't seem to be addressed at all: http://youtrack.jetbrains.net/issue/RSRP-196988?query=it
Is this a bug that will be fixed soon?