Specific textures revert back to Minecraft default when overlapping resource packs, as follows:

Block Textures
-> double_plant_paeonia_bottom
-> double_plant_paeonia_top
-> double_plant_blue_orchid_bottom
-> double_plant_blue_orchid_top
-> double_plant_grass_bottom
-> double_plant_grass_top
-> double_plant_rose_bottom
-> double_plant_rose_top
-> double_plant_sunflower_back
-> double_plant_sunflower_bottom
-> double_plant_sunflower_front
-> double_plant_sunflower_top
-> double_plant_syringa_bottom
-> double_plant_syringa_top
-> double_plant_sunflower_bottom
-> double_plant_sunflower_top
-> double_plant_sunflower_front
-> double_plant_sunflower_back
-> double_plant_fern_bottom
-> double_plant_fern_top
-> flower_houstonia
-> flower_tulip_orange
-> flower_tulip_pink
-> flower_tulip_red
-> flower_tulip_white
-> glass_black
-> glass_blue
-> glass_brown
-> glass_brown
-> glass_cyan
-> glass_gray
-> glass_green
-> glass_light_blue
-> glass_lime
-> glass_magenta
-> glass_orange
-> glass_pink
-> glass_purple
-> glass_red
-> glass_silver
-> glass_white
-> glass_yellow
-> glass_pane_top
-> glass_pane_top_black
-> glass_pane_top_blue
-> glass_pane_top_brown
-> glass_pane_top_cyan
-> glass_pane_top_gray
-> glass_pane_top_green
-> glass_pane_top_light_blue
-> glass_pane_top_lime
-> glass_pane_top_magenta
-> glass_pane_top_orange
-> glass_pane_top_pink
-> glass_pane_top_purple
-> glass_pane_top_red
-> glass_pane_top_silver
-> glass_pane_top_white
-> glass_pane_top_yellow
-> leaves_big_oak
-> leaves_big_oak_opaque
-> leaves_acacia
-> leaves_acacia_opaque
-> acacia_sapling
-> acacia_big_oak
-> planks_big_oak
-> planks_acacia
-> log_acacia_top
-> log_big_oak_top
-> log_oak_top
-> log_spruce_top
-> log_jungle_top
-> log_acacia
-> log_acacia_top
-> log_big_oak
-> log_big_oak_top
-> dirt_podzol
-> dirt_podzol_top

Item Textures
-> fish_clownfish_raw
-> fish_cod_cooked
-> fish_cod_raw
-> fish_pufferfish_raw
-> fish_salmon_cooked
-> fish_salmon_raw

This can be "patched" by doubling up the textures in the topmost resource pack, but it is a waste of memory, cpu/gpu cycles and time to do so.

This affects all new textures introduced in Minecraft 1.7.