This is most likely an incomplete answer and is based on my experience with Flarum thus far:
The ignore filter only applies when you are in the "all discussions" view. The Tag/Forum view grabs all the discussions under that tag, and then you deal with filters on the top left, eg: Latest/Top/Newest etc. Flarum's primary view options cater to mobile browsing, so if you only go to all discussions > latest you won't see your ignored threads.
If that doesn't work, let me know and I'll bring it up to SLC_96 and we cad do a big more digging.
