Using Gesture removes it?

I'm creating two actions:

The first consists on me holding down the right mouse button then pressing the middle mouse button.

The second consists of me holding down the right mouse button then pressing left mouse button.

When I go to "New Action" and create one of these actions I have to add two gestures to make either one of the actions:

The first one uses "RBUTTON_DOWN" then "MBUTTON_DOWN"
The second one uses "RBUTTON_DOWN" then "LBUTTON_DOWN"

My problem is: When I use RBUTTON_DOWN once, it will remove it from the list so that I can no longer use this gesture to make the second gesture. Can someone shine some light on why this is, and how to fix it?

It's not clear what your intentions are but according to your description it seems to me that you're not fully aware of how StrokeIt works and you misunderstand the purpose of the gestures and the mouse button triggering the gestures. So let's clarify this:

You create an action then you create commands assigned to that action. Then you assign a gesture to that action. That gesture will trigger the command. You have one dedicated button to trigger gestures. You can modify that at "Edit->Preferences->Draw gestures by holding". Each and every gesture will be started with holding down that button. When you hold down that specific mouse button and start moving your mouse (or click other buttons) you start the gesture which is ended by releasing the gesture trigger button followed by the action execution. Or it can be ended by gesture timeout in which case the action will not be executed.

When you assign RBUTTON_DOWN and MBUTTON_DOWN to an action that does not mean that your action will triggered by holding down RMB and pressing MMB but that holding down the draw trigger button and pressing down either of those buttons will trigger the action. They are each other's aliases. The gesture is removed to avoid it to be assigned to another action which would create ambiguous situations where StrokeIt would not be able to decide which action to execute.

Now, if you use RMB to start gestures assigning RBUTTON_DOWN to any actions is pointless.

I hope that answers you question.