I have this strange problem

I've just replaced all of the hardware on my guitar - tunes the guitar - done the innotation and action... But my 5th string (Second thickest) sounds lower than my 6th string?

By lower i mean deeper.

Any idea what is causing this?

Also, my 6th string seems too high... but its most likely just my ears.
maybe you reversed the gauges of the string for those two
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No theyre in the right order :S. My guitar tuner isnt recognizing my 6th string properly ive just noticed.
Pitch, the 6th string sounds the same as maybe the 3rd? but my tuner says all of the strings are correct. My tuner is having a hard time picking up my 6th string to.

Edit: I know the tuner works.
detune it and try retuning
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Tried that, i replaced the battery in my tuner (even though it said the battery was full) and re tuned - it sounds BETTER but it doesnt sound right.

Think im in need of a new tuner.
I like this new pickup though. ATM the way its wired - two single coils on the bridge or two humbuckers ^^.
I'm such a muppet - wound the strings to the machine heads wrong haha.