I REALLY hate setting up guitars also. My main guitar a Washburn X50 Pro which is basically a super strat with a les paul style fixed bridge with string through body. It is a real bitch to intonate.
The guitar originally came with 9's and I now use 12-52 strings and play in E standard, so I am thinking that could what is causing this mess.
The problem is that I can get all the strings to intonate pretty well except for the low E. When I put the bridge saddle for the sixth string behind where the the fifth string's saddle is, the 12th fret is about 20 cents sharp when the open string is in tune. The only way I can get the sixth string somewhat close is by moving it's saddle all the way as close the the pickup as possible. It definitely doesn't look right, and although the intonation is better than it was it still doesn't feel quite right.
Has anybody had a similar issue that can chime in?