Hello, the same happened to my system.
I placed a small shell script in /usr/local/bin and it worked fine when I call it from the Terminal.
After trying to load the launchctl command I got the "Load failed: 5: Input/output error"
My plist file was very simple and plutil check was w/o any complains.
[mf@Server]:/Users/xyz/Library/LaunchAgents $ launchctl load local.demo.plist
Load failed: 5: Input/output error
Try running launchctl bootstrap as root for richer errors.
[mf@Server]:/Users/xyz/Library/LaunchAgents $ plutil local.demo.plist
local.demo.plist: OK
After moving this script into /Users/xyz/ it worked fine.