After Effects render&preview doesn't match timeline I have a problem with rendering my video. Some layers are invisible until the next layer startpoint, despite the fact that their own startpoint is earlier, and some layers are left in the bacground of next ones, when their endpoint on timeline is already passed. Purging the memory/disk helps with all of them at a time, but once I run render, or even try to pre-compose - some of those layers are broken again, and preview/render picture does not correspond to what is on the timeline again.
The first step if you ever suspect After Effects might have buggy behavior is to purge the Memory / Disk Cache (Edit > Purge > All Memory &amp; Disk Cache).

You mention you already tried this, and that it cleaned it up at first, but then later on the buggy frames returned. In that case, you could consider temporarily disabling the disk cache completely:


  Choose Edit > Preferences > Media &amp; Disk Cache (Windows) or After Effects > Preferences > Media &amp; Disk Cache (Mac OS), and select, or deselect Enable Disk Cache.


Other things to consider:


Are you using any unusual file formats or codecs in your project?
Are you rendering to an unusual file format or codec?
Does the same project file on a different computer / operating system work?
General sanity checks (you aren't running out of RAM, disk space, etc)