I've got the following setup in two different rooms:
An FFC moves around the room with a Sword combo. Layer 1's Sword secret combo is a combo without the Sword flag, and animates for about 25 tics to register a hit but prevent multiple hits. Then it combo animates back to the first combo, which has a native Sword flag.
The idea is that each time you hit the target, the secrets should trigger once. In ZQuest, this works fine; hitting "S" successively moves through the tiered secrets.
But in ZClassic, after the first to third hit on the target, it immediately jumps to the last tier of secrets. Layer 0 only, it seems, because the boss health bar on layer 3 does not trigger.
EDIT - Aha. Took away the layers, and I think I see what's happening. Layer 0 has Secret Flag 16 all over it. The only Sword trigger is on the moving FFC. Yet when I slash the floor, it changes as though it were a slash combo, revealing what is under it. So you can cut your way down through the secret combos to reach the pit combos buried far below. BIZARRE, and unwelcome!
EDIT2 - Aaaand even more interesting, the floor only cuts away like that if Link is hitting the FFC. It's almost as if the FFC, if not struck in EXACTLY the right way, it doesn't register a hit on itself; instead, the floor registers it. Weird.