I am having a bit of trouble intonating the top 2 strings ( Low E and A ), all the other strings are intonated , but i cant seem to intonate these , saddles are all the way back, and still the sound is too sharp ?!

To intonate I tune the string , then I harmonic on the 12th , then I play the 12th fret, which has worked for me always , and now I cant ?!

BTW , the Strings are new , the guitar is the same.
Gear :Squier + Vypyr 15W / UCG102 + Picks = Awesomeness !
Have they always been sharp? If they've always been sharp, the nut could be cut wrong or need adjustment. try some graphite in the nut and on the saddle. Another trick would be to lower the pickup slightly on that one side and see if it makes a difference. Having it too close can occasionally cause problems. I've also experienced issues with those cheaper saddles if you they are too high or too low. Don't rule out bad strings, but it's kind of unusual to have two strings from the same pack be faulty.