Edited or removed recipes for modded/vanilla items.

NEI handles this just fine.

It should behave the same; both get the list of recipes from the game. The only obvious situation where I believe they'd differ is if you change worlds after opening the UI at least once but without closing the game, and the other world somehow applied a different set of scripts. In that case CraftGuide doesn't automatically re-build its recipe list, though there's a button in its options menu. Or, perhaps, if the scripts only run server-side in SMP, so the game client itself has the wrong recipes.

In what situations aren't they properly recognized?