I am using the arria V starter kit and I've had similar problems. I use quartus II 13.0.1.232, the standalone programmer v 12.1 sp1 build 243 and Win 7 x64. Documents in the board test kit directory suggest that the programming files were built using v 12.1 sp1 build 243 of Quartus.
- I restored the board to factory defaults, as described in the user guide.
- I ran the "qreg.exe --force --jtag –-setqdir" command from the "\qprogrammer\bin" directory for the v 12.1 sp1 build 243 programmer. This was advised in http://www.altera.co.uk/support/kdb/solutions/rd01292013_416.html.
- I ran "BoardTestSystem.exe" from the "\examples\board_test_system\" directory from the starter kit install location. This moaned about a missing Java directory. So I renamed and copied the jre1.6.0_07 folder from the "\examples\board_test_system\" directory to the location given in the dialog box.
After running Quartus II 13 the "BoardTestSystem.exe" said that the wrong version of Quartus II was being used. To fix this I ran "qreg.exe --force --jtag –-setqdir" command as described above.
On my setup the configure menu of the Board Test System GUI has the many FPGA configurations greyed out. As a work around, I closed the Board Test System GUI and then programmed the .sof files using the Quartus programmer for the particular demonstration mode that I wished to run. Once programming was complete I reset using the CPU reset button and started the Board Test System GUI.
Hope this is of help.
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