as far as I understand the flickering issue you are having is in your Internet browser, am I right? If this is the case the problem is related to the fact that you are using the OBJ exported by 123D Catch but, quite often, the normals of this kind of meshes are flipped and you should reverse them before uploading.
Also, before uploading the reconstructed mesh, it is strongly advisable to always import it inside a 3D editing softare in order to:
remove noise and un-necessary surfaces and eventually flip the normals
transform the mesh in such a way that it is oriented and scaled correctly (this is really important also because you will be able to add any augmented content on top of the tranformed mesh in the 3D editing software and when you will load it in your app it will be exactly where you expect it to be)
If you follow the above steps, the 3D geometry should be exactly where the real object is, otherwise something went wrong during the target creation process.
Can you confirm that not only the 3D geometry but also the pointcloud is in a wrong position? If this is the case can you send a screenshot? Does it look rotated by 90 degrees or is it in a totally different position with respect to the real object?
By the way, another important factor to keep in mind is that you MUST use the ARMedia Toolset app to take pictures of the object you want to track, please refer to this question for details: