Andrew, that doesn't really solve my problem if I'm gonna lose my MIDI output. I'm not familiar with RealTime plugins. Can you explain what they are?
The purpose of that was a test to eliminate the possibility of the problem being caused by some plugin you have (inadvertantly?) selected. I read through the thread a couple times and couldn't see this mentioned. The default would be to have the Coyote Wavetable as your default synth with no audio effect plugins chained. Reinstalling the program to a new folder as you did pretty much removed this as the culprit, however to be sure you could still do the simple test... just uncheck the box as mentioned and see if your song still crackles.
The problem is largely cured. When I run this one file that has five RealTracks, it takes almost one chorus of 32 bars before it's finally settled down to where there is a minimum of rice krispies now.
It doesn't sound to me like the problem is cured, since you're still getting crackling. However it does make sense, since the program will still be generating tracks while the song starts to play (using a different core), so you'll get higher CPU usage initially, and more likely to have problems. (FYI you can disable this "Speed up generation of tracks" in the RealTracks Prefs dialog.)
I suggest that you try disabling your network adaptor. Also disable wifi and bluetooth if applicable. Unplug your ethernet cable. Obviously this is just to troubleshoot. If it fixes the problem, systematically enable one thing at a time until it starts happening again.
Also, have you watched the Task manager during playback and have you noticed anything unusual? I have noticed that some people use a free program called LatencyMon, maybe do some research on that to see if it could help you.