This may be too obvious but when you plugged in that keyboard for the first time, did OS X ask you to identify it by pressing the key to the right of the left shift key?
If you didn't see that dialogue, just click the "Change Keyboard Type..." button in the keyboard preferences.
In case you don't see that button, you can force it to show up by deleting your keyboard preferences file and rebooting.
sudo rm /Library/Preferences/com.apple.keyboardtype.plist
The funny thing is when I tried this just now, I ended up with the same issue you described.
I finally managed to get things back to normal by actually pressing the ^ instead of the < key in the change keyboard dialogue. The keyboard was then identified as ISO/IEC 9995 which seems to be right.
Also, are you currently using Spanish as your input source? I noticed that there also is an Input source called Spanish - ISO. Maybe that is worth a try if the above doesn't help.
I managed to remap the Pause key with Karabiner on OS X 10.11. However, the current version of Karabiner is not compatible with macOS Sierra (10.12).
There is a preview version called Karabiner-Elements that runs on 10.12 but that allows only for very basic rebinding. I guess, there will be a new Karabiner release with 10.12 compatibility in the future.
