Ah, and this is why I said I don't like having my guitar down for a couple of days!
Wait, so you leveled and crowned the frets?
THEN you changed the nut?
How about, if you press at the 2nd fret, is there any air under the string as it lays over the first fret? The should be a canthair of air between the string and the 1st fret, between the nut and the fretted 2nd fret. If not, that could be culprit as to what your overall height is, all starting at the nut. Too low and you're bottomed out. As you press the string on the 2nd fret, you want to see the string just lay over the 1st fret, with a wee bit of movement almost hardly noticeable as you depress it to check.
Can you put the old nut back on and check that?
Did you do the black marker / take it easy on leveling stuff?
Is your neck / truss really straight? Any relief, looking down the neck from the nut to the saddles?
When you put the new nut on, how much did you change your saddles' height? Raise 'em or lower 'em?
Are you wearing hiking shoes or slippers? This can greatly affect things!
![Laughing :lol:](./images/smilies/icon_lol.gif)