Certainly could be your settings. Do you have anyone set on Rem. 4 def sub? That's generally a bad idea. Hal will remove him even if there is no one better at that position... In fact, he'll remove him even if there's no one
available at that position! And that can lead to chaos.
Conversely, setting defensive subs on the Team Strategy tab is pretty safe. Hal takes that as merely a suggestion, and makes a substitution when appropriate.
There was a recent thread about this topic:
viewtopic.php?f=6&t=647837