i was having trouble with Setpoint as well being very glitchy with explorer (not grabbing things correctly, double clicks, etc.) The best thing that helped me was uninstalling all Setpoint drivers from the system, unplugging the unifying receiver, installing unifying software on another computer, hooking up unifying USB receiver to that computer and then double checking that there were no phantom device pairings that tend to get "stuck" in the USB receivers flash memory. I noticed this issue when
I would end up with duplicate device installations under keyboards and mice in Device Manager, as I would have an extra USB input keyboard and/or mouse.
I would then hook the receiver back up to the original computer and first run Setpoint Installer as an Admin, making sure it replaced the defunct Logitech download manager drivers, USB input configuration drivers, unifying etc etc. There are 5+ special driver installations that correlate to Setpoint in the device manager if you have keyboard and mouse. Kind of ridiculous if you ask me, but these drivers are very sensitive to any sort of misconfiguration, mislabeled driver installs.
Once I had everything aligned with the Device Manager, I then changed the swipe to close variable in the registry for Wwindows 8 Apps, as Setpoint doesn't like to be sticky when grabbing metro apps for close, but works just fine once this metric was changed. I found an program called Appuituner or something that simplified modifying the necessary registry entries for this process, but not needed.
I originally thought I had a defecting mouse it was so bad with double clicking, as I would always try to troubleshoot this problem by repairing the mouse and shutting it off, pressing all the buttons down to try to clear any static charge it may have built up, but this was never a fix for me, but may work for others.
These problems bothered me for a couple weeks, so much so that it makes me paranoid that the problems will come back that I want to reinforce Setpoint in every way possible to prevent the nightmares Setpoint has been, hence how I found this thread as I want to run Setpoint with admin privileges.
I was not able to recreate the issue you are having with executing windows apps, not sure if this is because I changed the setpoint.exe file properties with app compatibility settings for all users to run as admin, rather than the exact methods you did, or because I have played around with gpedit loosening a variety of UAC and other windows permissions.