Texture packing help - Not all textures are packing

[Maclman]

As the title says, somewhat recently I've had trouble with making all the textures pack into the level.
Most times I try to pack(using both pakrat and VIDE) there will be 1 or 2 textures that VIDE will leave out then 1 or 2 different textures that pakrat will leave out of the level. :/
(note VIDE picks up the ones that pakrat leaves out usually and vice versa, but I've got a couple that aren't now)

Anyway, I was wondering if there's some new/different tool or method I should be using to make this work.
Thanks in advance to you all. :)

[B]Edit:[/B] they are all textures involving transparency if that helps