Lee,
Actually Im running 10.10.3 and LPX 10.1.1 here on two of my testbed systems and Im having no issues with crackling or whatever else with Software Instruments.... which is normally a sign of system overload... (given your audio tracks are fine)
So...
When you said it was Logic's SI's.. did you mean the built in ones or third party plugins (or both)?
What's Logic's CPU meter showing when this happens?
subsequently this is captured when bouncing to audio.
This is particularly strange that it would render to audio... as that indicates it's actual audio crackling rather than CPU/ Processing noise... which leads me to think that something else is going on here.. Maybe an FX plugin on the output or an aux being used?
As a quick troubleshooting test...
Assuming you have turned on all of LPX's Advanced Tools under Prefs (and if not you should!)
If you start a new project, with the Open Library checkbox unchecked...
add one Software Instrument track.. Choose one of Logic's built in plugins via the Instrument button in the track strip... choose a preset from inside the plugin... and then test.. do you still get this issue?