From which version of UC do you have updated, v6.xx?
When not starting the file compare by calling UC with a command line like uc.exe -b "File1.bin" "File2.bin", or using the shell extension (context menu in Windows Explorer), or calling UC from within UE/UES, but first start UC and then select the files to compare, you have to press the green triangle arrow between the file names named Go to execute the compare. Executing Go is also necessary when switching from text compare to binary compare. That gives you the possibility to set all options as you need for the compare before UC runs the compare.
You may think this extra Go is not necessary and UC should run the compare immediately after selecting second file. But this extra Go gives you the chance to verify if you have selected the correct files and if all options from the menu Options are set as you need for this compare before running the compare. This is very important for comparing really large files and for comparing large directories or directory trees. I agree that for comparing 2 files with just a few KB the extra Go is a little bit annoying.
I suggest to use the hotkey for this command as displayed at bottom of menu View which is by default Ctrl+F5.