OK, I found the cause of your problem and have a solution.
There's this function in the exe I have labeled as "byte FindEmptyMenuSlot( byte cIndex )" that looks for a place to put a command in the menu when building the command menu. This menu can hold 16 commands though in practice I don't remember it having more than 12. In this function, Slash-All, 2x-Cut, Flash, 4x-Cut and Attack commands are designated to the first slot in the menu so they'll override each other (If you have a Double Cut materia in an armor slot, that will take priority over a Slash-All materia in a Weapon slot). Magic/W-Magic are assigned the second slot, Summon/W-Summon the third and Item/W-Item the fourth. Any other command gets the next empty slot past the fourth.
FIX:
This takes two steps. First, the exe needs to be modded. Second, the materia needs to be changed (as you noticed).
Step 1:
Make these changes for the following commands (raw exe addresses):
Slash-All: 0x1CE2FD: FD -> C1
2x-Cut: 0x1CE30A: F0 -> B4
Flash: 0x1CE317: E3 -> A7
4x-Cut: 0x1CE324: D6 -> 9A
This will prevent that function from telling the menu building function that they go in the first slot.
Step 2:
Change the materia to type 6. Sub-Type doesn't matter.
Slash-All and Double Cut are the only type 12 materia. Change them to type X6 and they'll now be independent commands.