From the Intel Compute Stick side the option to have custom resolutions is not available, so in this case we would like to know how you are doing the custom resolution and what will be the purpose of it so we can consider investigate the problem that you are reporting.
Thank you in advance for your help on this case.
This is a little embarrassing. I've managed to resolve the issue.
It seems that some of our Compute Sticks ship with an option set in Display settings that causes this "over-display" issue. (Control Panel > Display)
For some reason, some of the units are set to Medium (125%), rather than Smaller (100% - default). Restoring this setting to Smaller resolved the problem.