Some remote controller commands are processed twice by Media Portal making it impossible to perform certain actions. For example, a pause command doesn't seem to do anything because the video is paused and then instantly unpaused. The controller in question is Logitech Harmony Hub working in tandem with IntelliRemote software which extends remote controller functionality by adding custom actions and scrips.
The most likely cause is Intelliremote processing iR signal and issuing a command to MediaPortal, and then MediaPortal also processing the same iR command and hence completing the action twice. After digging into MediaPortal Configuration utility I found a place to disable MediaPortal's ability to process iR commands directly. This can be found in Remotes and Input Devices > HID > Enable HID
Unchecking Enable HID option immediately resolved the issue
Windows 11 Pro