I know this has been a problem for others because I've seen the posts. However, never having had the problem, I didn't read them.
I just finished adding some controller data (sustain, mod,etc.) to a string quartet piece in Cubase SX3. Afterwards the file plays back with clicks and pops. I have plenty of RAM, should I set my latency higher?
Yes, try increasing the buffer setting of your soundcard. Latency isn't an issue on playback. This can get you some breathing room for your processor. Also, check to see if your controller data is extremely dense. Thinning controller data can make a big difference. At usual tempi I generally recommend limiting data density (for continuous controllers like mod wheel) to the 64th note when problems like this are encountered.