Remote Buddy doesn't change your settings when upgrading and there haven't been any changes to the Hulu Desktop Behaviour for what must be years by now.

The problem possibly stems from using a Harmony Remote - which is not supported by Remote Buddy. Therefore, when using Remote Buddy's support for multiple remotes and either a self-made or pre-made Harmony profile that sends the IR codes of multiple Apple Remotes, there are a lot of issues to be aware of:

1) the Harmony often doesn't correctly recognize Apple IR codes and will send badly formed and/or incomplete codes in these cases. Depending on whether a white or aluminum Apple Remote was used for programming, these are some of the problems to expect: 
a) the Harmony just plays back a recording, effectively sending IR codes for several button presses when you actually only press a button once. 
b) the Harmony only sends the beginning of the IR code, so that it sends the same IR signals regardless of whether you press a button short or long. This makes it impossible for Remote BUddy 
c) even when a code is recognized correctly, some Harmony models don't support long button presses at all for some of its buttons. The result is that the same code will perform great when performing a long press on one button, but will only send a short button press code when assigned to another.

2) Some pre-made profiles contain lots of these errors. The Plex profile that you may be using has these issues in particular: 
a) the codes for many buttons weren't programmed correctly, so that your Harmony will send wrong codes as described in 1a) and 1b) 
b) the codes assigned to many buttons often don't make sense (like f.ex. an "Up" code being assigned to a button that shows an arrow to the left) 
c) no code was assigned at all to some buttons 
d) while such a profile may work for Plex, which can prepare for such input, it's not suitable for general purpose use

3) Harmony Remotes can be configured to send sequences of codes for the single press of a button, which can lead to undesired effects when accidentally setting up your Harmony this way.

Therefore, please add Logitech's "Apple Remote" profile (which sends correct codes) to your Harmony Remote and use it with Remote Buddy to remove a big source of complex and hard to debug issues from the equation.

I've not been able to find any issues navigating the latest version of Hulu Desktop with the latest version of Remote Buddy with an Apple Remote.

Hope that helps.

Best regards, 
Felix Schwarz