There is no problem with the relationship. The problem is that the rule does not associate the two objects correctly.
Aware IM handles IDs of related objects automatically. You do not need to save the ID of CallRecord with CollNote. Instead, you should use the object name to associate the two objects:
CREATE CallNote WITH CallNote.CallRecord = CallRecord, CallNote.DateEntered = CURRENT_TIMESTAMP, CallNote.EnteredBy = LoggedInSystemUser, CallNote.NoteDetail = 'Call Closed', CallNote.NoteType = 'Call Closed'
You can still keep the ID of related object but the system will not make any use of it.
I am not sure I understand the other question:
a) Are you saying that "CallNote.EnteredBy = LoggedInSystemUser" in the above rule does not work? What is the type of attribute EnteredBy?
b) "CallNote.NoteDetail = CallRecord.CloseDesc" probably does not work because the above rule makes a different assignment: "CallNote.NoteDetail = 'Call Closed'"