I've reported this a dosen times now over years for years, Apple simply won't acknowledge this. This is tested and confirmed on three different computers and several versions of Logic (included the latest).
When using a Scripter plugin on an instrument track, if Freezing "source only", then you're up for some really odd things. Sometimes I get the recording from a completely different channels (say I frooze horn, instead if plays back trumpets). One time it created a Feedback-loop that nearly destroyed my hearing. Using the full freeze, there are no problems.
I've tried finding exactly what causes this, if it's connected to track stacks, or whatever. But I'm unable to pinpoint exactly what the problem is.
I've seen other people have the same problem. Freezing Source Only would be an excellent option to offload the hard drive when streaming large amount of samples, but still want to change stuff when mixing.