My Playback/Record pauses for 2-3 seconds..I have checked the Metronome , the relevant boxes are at O. The problem is not consistent though ...when looping everythings fine . 
I dont have a clue what's causing this glitch ..

Please tell us your system specs, soundcard, OS, what software you are using etc.
Is this equally with audio and MIDI? Any heavy VSTs involved?
It's worth the time to put your specs in the signature, so you don't need to write them every time. They're needed with every question anyway.

Ok ...I just found out this prob only occurs on certain sequence projects...I will check for VST load etc...thanks for the tip.

It seems to me that it is normal for Sonar to sometimes think for a second or two before playing. Look at your CPU meter.