My settings are to only download one file at a time. For some reason my scheduler is now releasing all waiting downloads at the same time.

Are you sure the local queue manager isn't auto-starting some of your queued downloads to use up more bandwidth?  That's probably what happening.

I tested the scheduler and it was starting up my downloads locally queued like normal, but then later the system will slowly auto-start more if not enough bandwidth is being used.

Go into Settings > Transfers > General and turn off Auto-manage slots if you don't like it.  But it usually does a good job for me.

Maybe you've got "Auto-manage slots" enabled, it will start queued downloads if your download bandwidth is underutilized. See if the function is enabled in Settings > Transfers > General > Auto-Manage Slots (for downloads).