On older quests, like 1.90, ladder only combos allowed the hookshot over them. Now, there is a seperate combo that allows both, and the ladder only combo only admits the ladder. This makes quests made with earlier versions incompatable because you can't use the hookshot with the ladder only combos.
My suggestion is to reverse it. Make the ladder only combo the hookshot/ladder combo, and make the ladder only combo the new combo. this should fix the problem.