I just mix down wave files with Sonar.
And Sonar just does an incredible amount of math operations in order to get the gazillions of numbers (samples) in a bunch of data files (audio stream) to "add up" to a final output. The more math you ask it to do (plugins are not devices they are computer programs that do their own math) the more likely you are to take too much real time to process the data. When there is not time to run all the numbers before the data is sent out, then there is a break in the data stream until the computer catches up.
One mechanism that programmers use to prevent this running dry phenomenon is to use a cache or buffer, that saves data in memory and releases it as needed. Increasing audio buffers in Sonar may help with your problem.