I do not know what causes this, but there seems to be some combination by any of the following:
often switching between japanese and chinese
using more then one browser at the same time with skritter
I am currently using ungoogled chrome for character writing due to skritter being bugged with firefox (i already opened issues for that), but i use firefox for everything else including studying reading, meaning, tone.
Also because i am learning chinese in parallel to revising japanese i quite often switch between the two. Today i have been doing this quite a lot and i had to disable study kana 3 times after suddenly being prompted kana again.
This might be related, but it also happened to me that while learning japanese skritter came to think i was learning chinese. This kept me learning the japanese vocab but ask me to write the charcters the chinese way. i.e with chinese stroke order and the small differences
this happened again. i was just using skritter normally. i did not actually switch between chinese and japanese this time, just kept using japanese since yesterday.
stroke order worked the whole time, but then suddenly it wanted chiense stroke order instead of japanese. then i refreshed the page because that is the only way to fix these bugs and now study kana turned itself on again.
hope this helps
edit: this time the setting turned itself on just after refreshing the page, but that does not happen every time, so i think I am still missing something