Comment 7 for bug 780659

Could you check any files in the (data) paths listed in 'Preferences > Misc > System info'?

Possibly unrelated, but I had earlier noticed that Inkscape parses the file contents of _all_ files in the 'palettes' directories (shared, user), and loads them if it detects the proper file format (for example: after editing a palette file in vim, the backup file *.gpl~ is loaded and listed as well after the next launch of Inkscape).

About the sort order: as far as I know, the user palettes are listed above the shared ones.