After Effects render&preview doesn't match timeline
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)