it's done this the past few days with a couple mods that lose their settings so i *assumed* it was happening for every mod too - i dont customize every mod, and lots of mods i use dont have options that would be immediately noticed if stuff changes.
anyway, i think i've narrowed it down to Prat. when i update it, it doesnt save changes i make in game. when i restore my previous Prat folder & savedvars files for it, the changes are fine. so i'm guessing the current version aceupdater is pulling from the server is buggy. :|
i've also just noticed (lol dont laugh) that since i manually delete portions of mods (like the kc_items bank/inventory/equipment saving modules) that AceUpdater puts them back >.< and when this happens, some settings get put back to defaults or something.
When I update my ace addons via the AceUpdater, my characters all lose their custom settings for the mods.
I use the !!!StandaloneLibs method, and update Without Externals. I also have AceUpdater configured to delete the old versions of the mods before updating to the new.
My .lua files seem to stay intact throughout the process too, which is weird.
When I manually update my addons (download zip files, unzip, delete old versions & copy in the new versions) all the settings are *usually* saved. I know sometimes authors change things that wipes settings, but this is usually rare.