Gradle desktop build not finding assets

Whenever I run my game using the DesktopLauncher I am able to find my files, but if I build an executable using Gradle I get an error that the files are not within the specified folder.

This may be linked to the fact that for some reason the assets I place into the Android project's asset folder, which is linked to my Desktop project, are being placed in the bin folder of my Desktop project. Currently to get around this I have a check that looks for whether I am executing as an Android game or Desktop (and applies a prefix accordingly, either "bin" or "").

You shouldn't be doing that check in your game code about whether to append the "/bin" folder path. Are you using the function Gdx.files.internal() for accessing the files in your asset directory?