Does the Scheduled task log file have anything related to the dependencies not running?
I apologize for never replying to this or updating the status. I ended up logging a ticket with LD support and it was eventually determined that this is a bug in version 9.5. I was told that this particular issue is fixed in 9.6 SP1. As a work-around, we created a package that included all of the dependencies wrapped in a single EXE, and we then deployed the EXE with the option to defer, which worked fine since there were no dependencies any longer.