When you enter new transactions in the system (e.g. journals), the system only validates them agaist "existing" combinations. The cross validation rules are only read by the system when it is time to create new combinations.
Lets say you have following combination in the system
001-10000-000
Lets say you enter a rule saying that the account 10000 cannot be used with company 001 any more.
Will system let you enter a journal with the following account?
001-10000-000
The answer is yes. Although the combination is in violation of the rules but it already exist.
Will system let you enter a journal with the following account?
001-10000-010 (note that the department is 010)
The answer is no. The combination does not exist in the system. As the system will try to create this combination, the cross validation rules will prevent it from doing that.
That is why after creating cv rules you must run Cross Validation Rules violation report. This report will let you disable all existing combinations that are in violation of Cross Validation Rules.