Usually crackling audio and overloads warnings are prompted by your system resources being taxed, or possible one particular spec being lacking. Not knowing anything about your system specs or exactly what you're doing in Logic when you get these messages, I could offer some general advice, though it sounds like it may include things you've already tried. I'll list a couple of things at the bottom of this post, but for a more educated guess you'd need to include your system specs (Mac model, year, OS version, CPU spec (speed/model i.e. i5, i7), amount of RAM, type of disk (HDD or SSD), size of startup disk and *how much free space* is available on that disk, Logic version, third-party plug-ins installed that might cause conflicts, etc); and a more detailed description of what you're doing in Logic (how many tracks, how many plug-ins, specifically how many *Instrument* tracks, is Flex in use?, etc; and other computer activity (other applications running in the background (not advised), networking activity in the background (not advised), etc)..
Lacking details, here are some "conventional wisdom" suggestions:
- Do a hard computer shutdown & restart and see if that has any effect (even if only temporary)
- Try a higher Buffer size -- depending on your computer that could be anything from 128 up
- Try shutting down any background activity (especially network activity)
- Try running Logic as a different user
- Try reinstalling Logic
- if there are third-party plug-ins installed, temporarily remove them and see if the issue goes away
- Try creating a brand new blank Project in Logic, start building up tracks, and see when/if problems begin..