The reason for this discrepancy is quite simple.  In figuring out why crystal therapy doesn't work when it doesn't, only the pseudoscientific claims of quacks have been tested.  When it is tested under other conditions, it has been shown to have a positive effect.  This has been accounted for as a placebo effect.

To say that something is a result of the placebo effect or is psychosomatic does not make it any less real.  Psychology is a real science.  Conditions like depression and stigmata are real, and have real physical effects, and sometimes physical causes.  So just because some kinds of crystal therapy only act on a person's psychology does not make the effects any less real or any less useful.

Simply put, we humans like pretty, shiny things.  We respond to colors and light refraction.  Even cats, birds, and other animals respond to the sight of light play on crystals.  It's natural for us to love light and to be fascinated by refractions.

We multi celled organisms also like heat.  Different crystals reflect, channel, and store heat differently.

We also know that an object related to a goal or objective is an excellent focus and visualization tool.

So we get many positive things from crystals: light play, color, heat channelling/reciprocation, and a focussing tool.  This is all before we get into mystical properties.

Let's be frank here.  The scientific community's conclusions about just about everything, are based on the premise of a universe without an intelligent, willful Supreme Being.  On the one hand, this is good, as it prevents a sort of mystical copping out when something isn't easily understood.  One can't just say that something happens because God makes it so.  One has to find out exactly what is going on through observation and experimentation.

Where this is great for most sciences, it is not so good for psychology or anything controlled by one's mind and/or soul.  Most people on earth have some kind of a belief system.  Even atheists have faith that their belief is true, that is not based on any actual physical evidence.

Since nobody has been able to prove or disprove the existence of God in a way that all mankind has to undeniably accept, then we are left with two options:  to behave as if we are all atheists, and totally abandon any behavior that is based on any kind of allowance for God's existence; or to go with what works for us as individuals, most of whom believe that there is or at least may be God.

If we believe that there is or may be, then there are a great many time honored traditions of healing and therapy that we should probably not discount based on a non theological premise.  The techniques and motivations just need to be updated.

First of all, any scientific justifications that are inaccurate, based on misinformation, or just plain lies, need to be removed from our field.  Crystals do not produce any more energies than any other stones.  What they were is exposed to alot of energy, which caused them to be crystals and not just regular rocks.  What we think of as regular rocks are amazing in their own right.  Crystals are just prettier to us.

So, the updated crystal therapist must be a mineral therapist.  They must explore how not just the pretty crystals, but many kinds of minerals, affect the mood, mental and physical wellbeing of various people.  A nice, heavy, rough bit of granite, or even a cement block, may help a certain individual focus on their goals and stay grounded better than any "lucky quartz".

Some people might benefit more from playing with sand.  Rock and sand gardens are known to be therapeutic.  An exercise of burying and finding a shiny crystal of their favorite color in a bucket of sand may help someone to find solutions to difficult problems in their lives.

If someone is having problems related to their confidence or body image, the sensation of rough diamonds (please buy only non conflict diamonds for this) lain against their skin might help them both to love themselves as they are, and make only positive changes.  Diamonds 
are beautiful even in industrial grades.  They may not be the most sought after for display, but they still have a glitter, and are still just as tough.  This definitely sends a positive message to the mind.

As conductors of soul energy, the benefits of crystals are well known.  When I am lending my strength to another, they are a good tool for staying focussed on a particular objective, and for filtering subconscious information into the conscious mind.

Yes, this is based on a theological assumption.  No, it is not science.  It doesn't really need to be.

...but is it pure faith?  Well, it's not really that either.  It's based on actual physical evidence.  I myself have benefitted from crystal and other mineral healing.  Others I know have as well.  However, nobody I know of has done well with just the crystals or rocks alone.  In all of the cases I'm aware of, the crystals were the tools of direction, focus, and enhancing the positivity of the situation, not the cause of the healing in and of themselves.

The field is wide open.  All one needs to do is to get out there and walk the path.  Walk it honestly, and you will find that your practice will be much more fulfilling, and much more effective.