As a sufferer of strabismus, what you are experiencing is not unusual but classic symptoms of strabismus. The brain does not have the ability to co-ordinate your eyes in unison.

When you have Esotropia, Exotropia or other alignment ailment, your brain will 'never' be presented with an image that can be fused to create the realisation of 3D.  As a consequence the brain will ignore the weaker eye and over time amblyopia will develop, reducing the vision of the weaker eye.

One solution to this is the use of prism glasses. The prisms refract the image passing through them to bring the images into correct alignment enabling the brain to develop the neural pathways required for stereoscopic fusion.

The initial hurdle to overcome here is that there is very little feedback to the brain as to the position of the weaker eye. In other words, while the strong eye is fixed on a subject or target. The weak eye will arbitrarily point in some relatively uncontrolled position. This is often referred to as an open loop system. Some may be able to alternate to weak eye. In this scenario feedback is lost on the stronger eye producing a similar mis-alignment.

For the eyes to work together, the brain will need to understand where both the weak and strong eyes are pointing concurrently (at the same time). When the brain has this ability, only then will it be able to ensure that the weak eye is rotated to the correct position to form alignment with the strong eye: i.e. when both eyes are looking at the same part of a subject. A capable (normal) cortex working in this mode forms a "closed loop system".

In this closed loop system, when you direct your gaze, the brain processes both eyes causing each eye to turn to the their exact individual "target locked" positions. In this scenario both eyes will maintain convergence and track the target, no matter if either the the head or target  is stationary or moving.
This occurs because both eyes are being adjusted by the brain, subconsciously to remove error in the direction of gaze.

Coming back to the question raised: while you are suffering with "sadly" an open loop system, your weaker eye will not necessarily track with repeatable results even after prismatic or other alignment. The brain will ensure the strong eye rotation tracks the target. Of course! this is the eye you are using. The weak eye however is just idly pushed into the approximate zone, while being completely ignored visually by the brain. 
Therefore even prisms which are set by the prescription are not 100% perfect every time and your weak eye is likely to settle in it's relaxed muscular position anywhere in a zone defined by the brain.

To develop fusion between left and right eyes in the vision cortex, the brain will need to be trained. In some cases this training will require that the eyes are stimulated with pre-aligned images over a long period of time. This can be weeks or even months depending on your own visual health. In essence it is nurturing the visual cortex with ideal imagery to form the linking.
Once that is achieved for some, only then can the brain start closing the loop and control the rotational position of the eyes.

Where does Equal-Eyes stands out over prisms?
There are two major advantages of Equal-Eyes over prisms and one disadvantage.

Advantages

• This can arguably be that Equal-Eyes can simulate prismatic correction with the advantage of being continuously adjustable
• Equal-Eyes can reduce the vision of the strong eye to force the brain to give controlled attention to the weak eye.

• Prisms can be worn during your normal days activity, even though they may be unsightly, they do provide a reasonable amount of correction, whilst of course, a VR headset is impractical.