Thank you for the suggestions.
tvolhein and TomHelvey are correct when I say that it does not matter where I start or stop.
In regards to SimpleManZ, I have tried reinstalling my soundcard driver many times without changer and I'm not sure which settings would effect the issue.
In regards to bvideo, using the Fade-in and Fade-out options help a lot with reducing the popping.
Is this just a standard phenomenon that occurs when using Sonar and related software or would better equipment be able to deal with it? (Is this something that occurs with others?)

Pops and clicks are usually the result of buffer sizes being too low.
Best to use an Audio Interface with provided/current ASIO drivers.
Stopping/restarting your Audio Engine can sometimes be a temporary solution.
I also stumbled on a solution to garbled audio at one time which was to toggle Input Echo (a couple of times).
For me also, it can sometimes raise it's head when system memory use is getting high (so resolve by 'usual methods' - close unnecessary programs, bounce tracks etc).

See http://www.cakewalk.com/S...-Playing-and-Recording

A pop can be induced at almost any point in a sound file by abruptly starting or stopping it. Most sound players take care of fading in and out automatically whenever you start or stop playback. The fade doesn't have to be much, or even enough to hear. The fact that you don't hear a pop shows that the player is fading for you. So playing and stopping the Sonar timeline should also be done with a short fade.
 
Other posters above were referring to the phenomenon of popping when the wave is cut where there is not a zero crossing. That is often a consideration when trimming audio clips, and is another case of the same phenomenon.

Pops and such are the result of:
1.  Your buffer is set too small.  Typically you should use a smaller buffer (128?) when tracking to reduce latency.  Experiment to see how low you can go, safely, then probably back up a tad larger.  Use a bigger buffer when mixing (1024 minimum required for Melodyne anyway).
2.  You are running out of CPU or system memory.  To make matters complex, CPU usage is a function of buffer size, where the bigger the buffer the less CPU required.
3.  There is an abrupt end or beginning on an audio clip.  Clips should always start and end with silence ... unless you are lucky.  The problem usually is related to the end of clip, where you have audio tailing off then suddenly dropping to zero.
4.  The zero-crossing problem alluded to above.

OK, I am convinced that cuts not at zero crossings would not create the pop at the beginning and end of each start or stop of the transport/now time randomly no matter where they are occurring and would not likely do so on ripped and imported known good audio. But the same mechanism for the pop can still be operating, i.e. a sudden change in signal strength to the analog audio chain or a sudden actuation of that chain. This is what happens if you turn up your monitors high then unplug them and plug them in again. A well designed 'bounceless' switch tends to prevent this on normal switching. It is as someone else noted the effect of rushing electrons, as the speaker actuator suddenly applies tension to the speaker. But there is another potential cause in the intersection of the digital and analog domains--DC offset. The former may be something you just have to live with, and if it is not being recorded in the final mix, but is just an artifact of play in Sonar should not be a problem. The latter is something you should be able to easily diagnose, and should be fixed as it can cause other issues, although it may not be audible once play has started.
 
http://manual.audacityteam.org/o/man/dc_offset.html
 
https://www.cakewalk.com/Documentation?product=SONAR%20X3&language=3&help=EditingAudio.22.html
 
 

I have the same experience when starting , stopping the transport. Never an issue when rendering. I just ignore it.

Thank you all for your help with this. Using the Fade options in the preferences helps with the popping, so I think it's just the sudden change from zero audio to full sound that causes the pop. I'll keep the zero crossing in mind when editing the audio.
Thanks again!

bvideo
Would this be relevant for your playback issue:
Auto fade when starting/stopping playback (search for this in the manual)
Edit > Preferences -> Audio - Playback and Recording.
Fade On Start (milliseconds)
Fade On Stop (milliseconds).
 

This is indeed the answer as you seem to have figured out. I discovered this almost a year after first installing Sonar and the improvement was massive. Much easier on the ears.
 
Thos pops on stop/start can really burn out your ear drums which makes it harder to focus on the mix... and for me it would give me physical ear/head aches.

bvideo
Would this be relevant for your playback issue:
Auto fade when starting/stopping playback (search for this in the manual)
Edit > Preferences -> Audio - Playback and Recording.
Fade On Start (milliseconds)
Fade On Stop (milliseconds).

I just did this and set the start to 2MS. It's like heaven!
 
No more pop.