I've been debating reporting this for a while b/c it seems like something that would be more of a pain for you guys than something that would actually make ZC better. Some of what I'm about to say here is just my best guess as to what's happening. There's a bug in there somewhere but I'm not sure exactly what it is or how to fix it? I don't think I've tested if there's been a change in behaviour since original 2.5.
All trigger flags are 'continuous' except for sword triggers (I only tested this with looping secrets and not tiered secrets in general, but I'd guess it does apply more generally). When a sword trigger is used in a way where the continuousness of other triggers would apply, in addition to not behaving in a continuous manner, for some reason screen secrets are not activated. It's especially strange when the strike trigger is involved, because its behaviour differs depending on whether or not you hit it with a sword. I think it's a good bet that this inconsistency with sword triggers was introduced along with the slash and slash/continuous combo types, but I don't know that for sure.
The fix might be to make sword triggers continuous again. Unless all triggers didn't used to be continuous in past versions. If that's the case, then the fix is to make non-continuous triggers actually activate screen secrets and then do the same that was done for slash combo types to all trigger flags (continuous and non-continuous versions of them all).
Maybe I'm just stupid and couldn't solve the room, but there was a room in Lost Isle I cheated my way through. It had looping tiered secrets that, if there is actually a version inconsistency and if the room was implemented in a certain way (I have no way to check how it was actually implemented), might have made the room unsolvable in 2.5? (I vaguely recall a sky dungeon, and I think the room was maybe near the upper-right corner of the map? But maybe plenty of people have played through Lost Isle on 2.5 with no problems and I'm just dumb for not figuring it out. The possibility of a version inconsistency that may or may not exist was in the back of my mind the whole time I was in that room and it was pretty distracting. Me being dumb is the more likely explanation here I think lol.)