Good lord.
I just opened a Project I transferred from another computer and found it horribly out of sync. When I started to check the others, they were also out of sync and I freaked out! All of the newer ones that I recorded on the computer I transferred to were fine---the older ones were not.
This helped! Thanks so much. I don't understand why it did, but it did!
EDIT: (if it's any help to anyone, I was transferring projects from Logic 10.4.8 to 10.7.2. My Plug-In Latency in 10.4.8 was set to all, in 10.7.2, it was not)