Offhand, my first thought would go back to my previous experience with putty and plink. The first time you connect to an SSH server, it prompts you to accept the private key, and then stores that in your user profile. Keep in mind that when you run things from a kaseya proceedure it runs as the "System" user by default. My guess is that it's failing to actually do anything when run as system because it's trying to prompt you to accept the key. My first suggestion, though I can't really test it from where I am right now, would be to add the -batch argument to the plink command line as that specifically disables all interactive prompts.
I'm not 100% certain that is what is going on, but it's my first guess. The other option would be to "use credentials" to specifically get your script to run as a specific user and ensure you have accepted the key previously.