Thanks for the help, PreSonuSupt4!
Your workaround worked perfectly on 2 of the 3 songs that were having this problem.
On the 3rd, I did all the same deleting, adding, making default with the inputs, and the problem was still there. I then turned off the low-latency monitoring on the main output bus, and un-solo'd the main bus. Then re-enabled both, and voila! It looks like the issue with the inputs may be related to the zero latency monitoring, and this was my suspicion but I couldn't figure out how to reset things. I do know this issue didn't start until after upgrading to 3.5.1. For what its worth, I am running Studio One Artist 126.96.36.199560 OSX x64 (Built on Jun 23 2017).
Anyway, I am back in action now. Thank you!