I have now got the inbox rules to work again. Thought I would share with everybody how I got this to work.
I haven't found any good way to debug the server rules on the server but I found this out.
By reading some code. ;-)
1. All rules are resaved everytime you move a rule up and down.
2. The rules are stored in the Calendar Profile document
3. You can max have 100 rules per inbox
4. The Calendar Profile document can start acting strange due to policy changes if you use them
What did I do to make my rules work
1. Checked that I didn't have 100 rules
2. Created a rule based on sometime in a title of an email
3. Placed the rule at the bottom of my Rules list, so it would evaluate last
4. Tested that the rule didn't work
5. Started to move the rule up and sending one email per move
6. Found the faulty / corruped rule and removed the rule
And now everything work great...