Weird Stereo delay going on ?

Hey guys, i was recording fine in logic pro x then i unplugged my guitar to tune up and when i plugged it back in there was a weird stereo delay thing going on. It's not latency as the signal comes out of my left monitor as soon as play a note but is then delayed like an 8th note before coming out of the right monitor Have no idea what has caused this as all i did was unplug my guitar to tune up. There are definatly no plugins being used yet on any of the channels. It only happens when i click the input monitoring button once i unclick that the delay goes away but obviousy i can only then hear the guitar out of one speaker. And when i switch from stereo out to mono there is still an 8th note delay but it just happens in the left speaker ? All the takes i have already recorded playback fine.....im kind of stuck here....any help is apreciated ?

Im using the line out of my amp to get the guitar sound in to a USB pre-amp straight in to Logic pro X.

Thanks