You could try the process of elimination.. Deleting certain rules until you find the one that is conflicting.. and modify it.
That's the only thing I can think of, Someone else may be able to help you. Though I do think the problem is within the rules because it worked on default.
If you find the rule that is causing Freezes and start up difficulty's it might be a good Idea to post which rule caused this so that Someone from comodo might be able to fix, or not allow the user to create such a rule.
Kyle
I cannot confirm that it would have worked with default rules since I cannot run them due to security issues.
I don't agree on your theory about a rule causing this, however:
why would D+ freeze when switching modes?
why would D+ block things it shouldn't, and
why does it "forget" to log things?
why is the Active Process List not working?
These are things which have nothing in common with any rule. They are program related.
Of course I didn't change any rule regarding CFP itself, so it shouldn't keep disturbing itself, I guess.