I'm having trouble figuring out what you mean by "damaged" (which is the heart of the problem with AE), so without using metadata numbers or a screenshot I'm having issues figuring out what you're actually doing.
However, what you're probably experiencing is AE defines damage as 0% at fully repaired and 100% at fully broken. This is opposite of metadata (and heat), which counts up as you damage an item.
EDIT: If you want to test this for yourself, go into a creative world and get a 5/12 durability and a 2/12 durability wooden shovel. Filter on the 2/12 durability shovel and split damage at 75%. The 5/12 durability shovel doesn't match because it's not on the same side of 75% damaged as the 2/12, even though the metadatas are on the same side of 75% of their max value.
EDIT 2: tl;dr - heat counts up while AE counts down. If I've read your post correctly, once the coolant cells hit 75% AE goes "Well, this one thing is 99% damaged and one is 25% damaged and he's splitting at 25%, that matches". Change to split at 75% for better results.