From your file I was able to reproduce the issue. I have submitted a fix for the Installer issue. You can either sync-up to the HEAD of the SVN repository or you can overwrite your device/XDLRCParser.java with the new file I have attached.
I rebuilt that particular database file that you had listed in your version of TestS6Pins.java and the problem is still recurring.
I believe the problem might be somewhere in the Device.populateSinkPins() method that happens during database file creation. The SinkPins are not getting populated properly and this is causing the problem. Unfortunately, this function is a bit complex and it appears that I only got it working for some families.
Unfortunately the demands of life and my schedule will make it to resolve this issue and it may have to wait until later next week. However, feel free to take a look yourself (load it up in the debugger) and you might be able to find the problem.
I'm sorry I can't be much more help at the moment. Feel free to reach out with more questions and I'll try to answer them.