Guitar not tuning right

Hi
I was playing my guitar, when I realized that it sounded a bit out of tune, so I grabed my tuner and tuned the guitar. I went back to playing the same thing, but the guitar sounded out of tune. I double checked with the tuner, who showed my guitar to be tuned!!!!
What is going on with my guitar? any Ideas on what it could be and how I could fix it?
Thanks

Sounds like the intonation may be off, look for some setup resources on how to set the intonation.