if deleting the superpallette is fixing it (at least temporarily), then it sounds like you have a terrain set that is corrupting your superpallette file, if I remember correctly each terrain set adjusts that file the first time they're set (after the superpallette file is created) in the editor.
Does it breaking usually happen after you have switched terrain types in edit mode, or after using edit mode on an existing map that uses a different terrain?
If so then try some different terrains until you find the one that causes the issue, then remove the files for that terrain, verify (if they're default files) or download them again (if they're store files), and see if switching to those terrains still causes the problem.
i5, NV960 2GB, 16GB memory, 2x 2TB Hybrid, Win10.
i3 , Intel integrated graphics, 6GB memory, 512GB Generic SATAIII Win8.1.
Intel Celeron (duel Core), Radeon integrated graphics, 4GB memory, 180gB Generic SATAII, WinVista.
Q6600, Intel integrated graphics, 8GB memory, 512GB Generic SATAII, Win7.
