I use a capo a bit and having issues with my US Strat. The intonation isn't perfect but pretty close and normally plays well without a capo. I usually capo up 2nd or 3rd fret and the low E string sounds a fair bit out of tune. Have tried putting it in all different positions, up close the the last fret, back towards the rear fret.....on a slant etc. It's a good quality capo too and I tried my friends also still pretty much the same thing. I had a look to make sure the capo wasn't pulling the E string sideways or something looks ok. The frets aren't 100% but they're not bad and its doing it in the 1st, 2nd and 3rd fret positions. I have had this issue before with some electric guitars where they just don't seem to capo well. Is there anything I am missing or something I can try?