Hey, I've been working on a cover of a song, (Even If She Falls by Blink-182) and I've been trying to transcribe the drums from the song into midi. Now due to the drummer of the band this process is tedious already, haha, but when I try to take a segment and copy paste it, say a set of sixteenth notes on the hi-hat, it pastes, but it pastes several bars further in the song. It seems on and off at the moment as well, but more often than not it's doing this. I'm using Sonar X3, editing in the Piano Roll, and using SL-Drum Kit as my synth.If there'a way to stop this, I would be very happy, thank you.

Hi, and welcome to this forum. 
Which version of X3 do you have? (Home, Studio or Producer) If you have Studio or Producer, you could use "AudioSnap".
https://www.cakewalk.com/Documentation?product=SONAR%20X3&language=3&help=AudioSnap.01.html
There is also an option to extract MIDI from Audio with AudioSnap if you have Studio or Producer edition.
https://www.cakewalk.com/Documentation?product=SONAR%20X3&language=3&help=AudioSnap.15.html
All the best.
 

Also check that "Always Import Broadcast Waves At Their Timestamp" is unchecked. It is located in Preferences (P), File, Audio Data.
 

Thank you Zargg! The "Always Broadcast Waves at their Timestamp" seemed to fix it. I was using Producer, by the way, and I'll have to look into the AudioSnap thing, looks very useful for all this. Thank you again for helping me, I was starting to get really frustrated with the PRV, but now that's it's working things are smooth sailing again.

You are very welcome  
If you have any more issues, just come here and ask.
There is an amazing amount of knowledge among the members here, and always someone willing to help. 
It is also useful to put your specs (SONAR version, OS, cpu, RAM, Audio Interface / sound card, etc) in your signature (see mine below), as it helps when someone is trying to help.