Downgrading uTorrent back to v3.2 seemed to fix this issue for me.

Looks to be something with downloading from magnets that caused "Run Program" not to work, but it seemed to execute fine through my RSS downloader.

Hey there, For the past few months, the uTorrent run program feature doesn't seem to work for movies, but it's still working for TV Shows. I realize this may be more of a uTorrent issue, but I'm hoping someone has run into and resolved this issue here... Here's the log when it runs for a TV Show ...