Epic Fail intonation

So yesterday my D string on my Strat was sharp so I set the saddle ALL the way back (I even had to take off the spring pushing the saddle forward) but it was STILL Sharp out of intonation.
I grab it today, The low E is sharp at the 12th fret and the D is Flat at the 12th?
I have the back springs tighened all the way and the whammy has not been used. The nut is clean, level, and lubed (with graphite). So what could cause this?
(Guitar has been in controlled humidity and not been anywhere except its stand and in my hands, all parts are secure and have not changed. Neck is completely straight.)

Change the strings.

I had the same problem before.

If that doesn't fix it, take it to a shop.

I agree,a fresh set of strings. Unless you just changed
the strings,and they are still stretching,or your using
a different gauge as before.

1. Change the strings
2. Tune to standard tuning
3. Adjust tremolo/bridge float by adjusting springs in the back (I like mine adjusted so I could pull up a half tone on the whamy)
4. Set saddle height
5. Set intonation

Note: everytime you make any type of adjustment/s on the saddles whether it be height or intonation, retune all strings to standard pitch then start over

when you buy 10 packs os strings you can pay less than 4 dollars a set.

Four dollars a set eh nullnaught?

lemme see 4x10=$40 I would do that,buts kinda a
large investment when you have no income(me being 16)

Or, you could look for a string endorsement and pay less than that per set ;)