Please log it as issue as it is a defect.
As a quick work around use non absolute path abd substitute it with the absolute one in the WxsGenerated event handler. It will be very helpful for you if you have a look and compare the two wxs files generated for both working and not working scenarios.
As a quick work around use non absolute path abd substitute it with the absolute one in the WxsGenerated event handler. It will be very helpful for you if you have a look and compare the two wxs files generated for both working and not working scenarios.