I might have found something related to this bug.
tl;dr version: In Aseprite v1.2.16 we’ll simplify the behavior of default docs settings: if there exists a .ini file storing the preferences of a sprite (in the preferences folder / files/ … .ini location), the defaults settings for that sprite are not modified.
Long version: If the global setting for the visible grid are changed (e.g. View > Show > Grid menu option is selected when there is no document opened), then that change could set the default of the other sprites (even when the sprites were already opened in the past so they have their own preferences set). This is more visible in the File > Export Sprite Sheet preferences, e.g. if we create a new sprite, export a sprite sheet from it with the “Trim” option checked, that option is saved as the default option for future files, but if we open an old file that we’ve exported but it doesn’t specify the “trim” option (not false nor true), the new default will be copied, so the trim option will be enabled for a sprite that was exported in the past with the trim option unchecked.
This was found with a re-design of the Export Sprite Sheet dialog and thanks to @KashouC for reporting the bug 
and I guess it’s related to this bug too.
Commit fixing this (supposedly): Don't set preferences with latest defaults if there is an existent .i… · aseprite/aseprite@002abc9 · GitHub