Weird Intonation problem

[Bobby T]

I have a strange intonation issue I have not seen before I hope someone can explain to me.

 

I have a Schecter Stiletto Extreme-4 that I love playing.  It is the easiest to play bass I have owned. I am very much an amateur. 

 

Recently I noticed my intonation was off on the E-string, so I adjusted it using the bridge adjustment so that the open and 12th were both in tune.  The problem now is every note from G to D is flat.  

I don't understand how this can even happen, unless maybe it does this if the neck is bowed backward? 

To add more strangeness, the A-string is a little like this. D-string is fine and so is the G.  Which makes me wonder if there is a twist in the neck.  I have not measured anything yet.  That is next, maybe just a complete setup is needed?  

Any ideas?  Thanks