This appears to clearly be a bug in Hulu Desktop. Please contact Hulu and file a bugreport with them to alert them of the issue.

As a temporary workaround until Hulu fixes their bug, you may want to try using the actions from the Virtual Remote at Prefs > Mapping > Hulu Desktop to emulate an Apple Remote when Hulu Desktop is active. Depending on what OS release you're running, this may or may not be a solution: Hulu Desktop uses completely outdated, driver internal/OS release dependent code for their Apple Remote support. In consequence, Hulu Desktop's Apple Remote support will simply not work on many systems.

I've already contacted Hulu about their Apple Remote issue in the past and pointed them to an easy, quick and free (!) solution. I've not gotten any response, yet.

Best regards, 
Felix Schwarz