Well this issue is occurring for me on Windows 10 x64 and does not happen on Linux (thanks to @sergio-br2 who tested that out)
Anyway, as I showed in my filed issue on GitHub, this is my problem:
What could be the problem here? Is there a new setting I could have missed in 1.4.0 and 1.4.1 that were not in 1.3.6
The pointer in every version of DeSmuME works in 1.3.6 that I have tested (October 2016 - present)