First time that happened is when I was using friction shifters and a sram rear mtb derailleur as there wasn't enough pull for the sram. Just happened on the shimano alivio one I got to go with some friction shifters though which is odd but I think that might be the hanger though. I didn't try too hard though because I didn't want it to go into the biggest cog cause it is a bit too close to those spokes the chain likes to eat on the cruz mess.

The 5 mm difference is the dropout difference. Cassettes cogs are the same width. What brand of shifter and what brand of derailler? You can't just mix and match. If you put a SRAM with a Shimano, it has to be the right SRAM, one that's Shimano compatible.

Been busy but let me explain my set up better. I have a V3 with all SRAM goodies. I have the twist shift X5 shifters . I had a X5 9 speed rear Derrailuer that worked fine and a adjusted out fine. Both the X5 and X9 say 1 to 1 actuation on the side of them. Reading the SRAM site it said if its 1 to 1 it should work.  
 
The problem with it is the throw to the large cog is too much. It seams like I have to screw that mechanical adjustment almost all the way down to get it to pull it in far enough to keep it from overthrowing into the wheel. When I do this and get the large cog lined up perfectly the adjustment screw is apparently to far in becuase when I shift all the way down to the small cog the adjustment screw for the large cog touches the inside of the frame on the back of the X9 causing it not to set down all the way. If you look at the small cog adjustment screw there is even a small gap so I new something was hitting.  
 
It looks as if the lip on the back arm of the X9 does not come off the back arm enough causing you to screw the adjusment screw in farther then you should. Thus my theory that maybe the different widths would cause the cogs on a mountain bike to be 5mm further away from the hanger and thus you would need less adjustment.  Heck my shifters shift the X9 perfectly and it is very crisp. However the mechanical adjustments are off some how. Orrrrrr I got a bad derrailluer that wasnt machined right or something weird but I doubt that is the case. I bet a road vs MTB is just enough differrence to cause my issues. Thats what I get for trying to save 15 bucks. LOL  My wheel guy loves me I am sure.  I am not sure on any of these theorys and have not called SRAM yet but will soon and see if they have an answer.
 
Anyone need an X9 for their mountain bike cheap. LOL Used once.

Well after chatting with the ebay store she said send it back for a refund. I guess I will take the whole thing to my bike store adn have them do it so its has some sort of warranty.

Bike shop had it back in one day. New X7 and my old Velocity. Shifts great and the mechnical adjustment screws look right in the cage. To me it looked like the X9 was drilled wrong or had a bad angle when they drilled it.