That's so easy I hesitate, but here goes...
The audits you decribed are being used to do nothing more than submit the organization to continuous beatings....Who do you know that really likes that?
You have described a reactive, negative, relatively non-value added activity and that is happening is what is being sought, non-cooperation and resentment. You're getting what you ask for...Enjoy it!
I admit, there are occasions that can mandate looking for where things are wrong, finding mistakes, undercovering problems, but not all the time! Sheeesh, who wants to participate in beatings?
You wanna add value and gain cooperation? It's so easy most "professionals" tend not to believe it, and here it is....Audit for what is right or what is supposed to happen. This can be called looking for "conformity". When we look for conformance as our goal the taste of the audit changes, we are looking for good, not bad. It is in the quest of "conformity" we will find the good or correct, and where we will find the broken or non-conformity, and we will find the "real-deal" and that's the stuff that may be having some difficulty and can be made better..."Opportunity"...Value Added stuff, or chances where we can do something entirely new and different, ....also Value Added.
When we focus on finding non-conformity, such as in the audit methods you described, we will almost, without fail, ingore those things that are not either correct or wrong... We will just see Black or White, nothing else...No Value!
Auditing is kinda like a story I tell about an old dog and it's master, and here it is....
Suppose a person has an old dog. Everytime that person approaches that old dog the dog will rise, wag its tail and smile (Check it out, dogs smile). The dog loves its master and shows that love in its greeting and action.
Now visualize the following....The master upon his approach and when being greated by the friendly old dog starts talking harshly and kick the dog when passing by and continues to do so from that time forward. Everytime the master passes the dog harsh language and a kick, harsk language and a kick.
After a while the dog will no longer rise, smile and wag his tail, he'll just huker down waiting for the kick....But here's the deal, the dog still loves his master...Dogs are very forgiving.
Eventually while in the process of kicking the dog, the dog will rise and bit the master. Why? Because no matter how friendly and regardless of its love for the master, that friendly old dog will get tired of being kicked and will strike back in defense.
Now change the story...The master is the organization and the audit methods it uses, and the old dog represents the people within the organization.
This may seem pretty simplistic to all the wiz-bang experts, but it's a fact.