Tomas,
I actually have a development installation that has the same problem with the shortcuts (on Windows, I assume you are the same). I'm not entirely sure what is happening, as you have noted, there really isn't all that much to go on, so I moved on. On the bright side, it's much easier to track down the issue if I can replicate it so hopefully I can figure it out sometime this week. In the meantime, you can try to recreate the shortcuts by re-running the desktop-app command from the installation instructions. It didn't work for my, but you may have better luck.
As for the DAQ, that is pretty concerning. Do you happen to know what your previous versions of labscript-devices, blacs, and labscript-utils were before the upgrade? And to be clear, you are on the current latest via the conda repo? I will say that opening NI-MAX with BLACS open will always cause problems since accessing an NI DAQ via either program blocks it from being accessed by the other. This is by design.
Obviously, not actually getting changes on the outputs is a bit more strange. Just to confirm the steps you are following, you start BLACS (NI-MAX is closed), it claims good connection, but outputs don't update under manual control. You reload the tab, which gives manual control, but then you try to run a shot and you get the comms error. Given the error, it appears multiple tasks are being assigned to the same outputs, which really shouldn't be possible under normal BLACS operation. Is NI-MAX still open in the background? Assuming that isn't the case, there haven't been too many changes to the NI-DAQmx code recently (depending on how big of a jump in versions you did), particularly with regard to the DIO stuff. Still, stuff happens and it's hard to test every single DAQ card these days. I'll poke around the recent changes and see if anything jumps out at me while I await your response.
-David