I have tried to use the tool on Ubuntu 14.04 kernel 4.4.0-84.
The device detection hangs and quits with No PICkit 2 found.
After a debugging session it turned out that no response is received after queriing the GETVERSION command.
After some wireshark dumping it turned out that the Windows software does not sends the CONFIG_VENDOR request.
After removing this code snippet the tool works as expected.