I have the same Problem with "toggle deploy surface control" for wings but found a way to prevent this from happening.
The action seems to be serialized, meaning it applies the toggle for each part listed in the command, but the symmetry still applies. In other words, if you have an even amount of symmetric parts, the toggle will be applied for ALL parts n-times and thus cancelling out.
You simply need to only have one of the symmetric parts in the action manager and you're good to go