I don't know if it helps, but we measured the time resolution between two independendly running v3 boards using a single PC (latest software) in Linux. (http://arxiv.org/abs/1405.4975)
You start the DRS DAQ program with only one USB board connected, first. Afterwards connect the second board and start another session. If you externally trigger (global) both boards with less than 1 Hz, you can garantee that both programs save the same events independently (from two individual DRS boards).
I never had in mind running two systems in parallel, that's why the code claims all interfaces when started. You have to dig into the usb code which is located in musbstd.c at function musb_open(). There you will find a line libusb_claim_interface() which requests exclusive access to the usb subsystem. The code is there because I copied it from some standard example for the libusb library. You have to read the documentation for libusb (http://libusb.sourceforge.net/api-1.0/) and see if you can get rid of that. Probaby you have to claim/release the interface on each access, but I never tried that.
we want to run two instances of our little DRS DAQ program but obviously the first instance started always claims all DRS boards for itself and the other one exits with an error. The 2 boards used in the example below have the serial number # 2413 and #2414 and are v5 boards.
The first one:
mathes@ikauger5:~/src/DRS4/Cpp> ./drsdaq -b 2413
DRSController: found board with serial number #2413
DRSController: found board with serial number #2414
DRSController: using board with serial number #2413
DRS type: DRS4
Board type: 9
Serial number: 2413
Firmware revision: 21260
And the second one:
mathes@ikauger5:~/src/DRS4/Cpp> ./drsdaq -b 2414
musb_open: usb_set_configuration() error -6
musb_open: Found USB device 0x04b4:0x1175 instance 0, but cannot initialize it: please check permissions on "/proc/bus/usb/1/7" and "/dev/bus/usb/1/7"
USB successfully scanned, but no boards found
How can our goal be achieved?