. . . The effects, like always, were tested extensively in the "lab". That said, sometimes things don't work the way you planned once you've got them all in the same space together.
Often a special effect will be tested in isolation to optimize for what it requires to be 100% effective . . . and when you're developing different effects for one environment at the same time, you're not always able to account for the way they will affect one another until you're "in the field" and they're already affecting each other. At which point you only have time and money to try to compromise as best you can and try to optimize for each elements' effectiveness before going totally public. That's not always enough time to make everything work they way it did in the shop.
A famous example of this is the original Hatbox Ghost at Disneyland's Haunted Mansion - the effect was Blacklight-based and worked properly in the studio, but was thwarted in the ride by the ambient blacklight in the scene. Attempts were made to renegotiate both the amount of blacklight in the scene and the extent to which the figure's effect was dependent on blacklight . . . ultimately it was decided that the best answer was to pull him from the scene. It would have been simple enough to account for all this in the studio if it was known they'd have to account for it, but you don't know what you don't know.
Part of the blessing and curse of special effects - especially exciting ones - is that they're often working prototypes and being invented as they go. For all the tech there is now to figure things out before hand, there are still blind spots that don't become visible until install. "In theory, there is no difference between theory and practice. But in practice, there is".
I say all this with no inside knowledge of how install is going at MMRR - but it wouldn't surprise me if the 2 1/2D effects that sold this ride aren't as compelling in the attraction as they were at Imagineering. It would not be the first time something like that has happened. Though it would be unfortunate just the same.