weird behavior

I would be less a slave to "walks" and more going back to square one and re-desensitizing the walks.  Forcing won't work -- I would change where you walk and how you walk.  Not sure why you use a car but I would simply start from home and literally go two feet and go back home.  (or back to the car if that has to be your base of operation).  But when you allow her to call the shots you reinforce the fear.  By trying to have your own "goal" of how far to walk you push her too far and it becomes a contest of wills.  YOU have to cut it off before *she* is ready -- you call the beginning and end.  Even if you have to exercise her in another way at home - simply tossing a Kong in the yard or even just tossing a kibble around in your house or apartment so she gets exercise that way.

There is honestly nothing "holy" about a walk -- and making it into a contest of wills doesn't do a thing.  She has to re-learn confidence that she's gong to be 'ok' while on the walk. 

Have you tried a "storm party"?  Part of this is that she is holding to her own judgment rather than yours. I try -- during a storm -- to let the dogs see that *I* can judge when a storm will begin and end ... and *I* am calm and confident and they can take their cue from me.  If you act afraid of the storm yourself (even if it stems from just getting wet and that being unpleasant for you) -- then the dog feels it has basis for the fear. 

My dogs know that a storm is nothing more than a big excuse for a PAR-TEEEEE at our house.  They know Mom is NOT scared, but rather kinda gets "into" the whole storm thing -- "whoa -- look at THAT one" ... etc.  But if you are in "control" of the storm and can sort of predict the middle and end of it (wow -- I only got to count to TWO that time -- it's going AWAY!!!";) the the dog can feel their fear is baseless and they can TRUST you. 

One of the things *I* would do is pretty well embrace a storm -- I would avidly watch it and expect the dog to join me with tons of treats.  Yes -- the use of valerian and calms is great -- BUT you use that then as a training time.  With the basis of the calmative you THEN show the dog that a storm doesn't have to be feared, but rather can be almost enjoyed.  I shut everything off and we use it as a time of fun.  They get my attention (along with the storm) and we have fun together. 

Now at first are they having fun?  no.  BUT it comes eventually.  But if you respond in fear (or even in distaste -- which can be interpreted the same way by the dog) then they see their fear as justified.

 We use the car because we go to the parks.  She use to love those walks.  She goes for 3 walks a day.  She's a high energy pit bull mix.  One of the walks is around our neighborhood.  Now she doesn't even do her "business"  in our backyard.  If I didn't take her for walks she would hold it till she couldn't hold it anymore.  I think the "holding" is from being in a shelter for 1 1/2 years.  I've tried getting her happy and in "party mode" when a storm comes, but she doesn't go for it.  She won't take any treats or drink any water when she hears or thinks that she hears thunder.  Also, how do you have a party at 3 in the morning?  I know she came from the shelter with this fear.  They told me about this.  It was an outdoor shelter and when they finally realized her great fear they would put her indoors when a storm was coming.  But, they were not there in the middle of the night to do that and at other times.  I now try to walk her where other dogs may be because then she thinks of them instead of her fear.  I guess I am making to much of the "walks".  It just her energy level.  By going for many walks she has turned into a wonderful and even peaceful dog around the house. 

I'll say keep up the good work with the walks. I totally understand what it means to not to walk your dog even for only one day. As an Alaskan Malamute owner the walks help not to have my house destroyed :)

Buy a "Nature" CD that features thunderstorms and play it on the lowest volume until she gets used to them and then keep playing. Let a week pass with the same volume and then turn it up just a little bit and repeat.

Find what she likes the most to do and do it with her while the CD is playing, maybe at a lower volume she will actually eat. Do not say "it's ok" if she shows fear because then you are nurtiring the behavior. After a while she will realized that the thunder actually dont cause any harm

It tends to be more than just "noise" with storm phobia-- it tends to be the electrostatic charge of the storm and an outdoor kennel would have caused that to resonate big time.  Desensitizing with the storm CD might help a bit, but generally it's going to take time to extinguish such a behavior and gain her trust again.

All it takes is ONE bad turn to form a behavior or generalize it like this.  So you keep working on it. 

How do you have a storm party at 3:00 a.m.?  It's all in your own personal enthusiasm.  Keep a bag of something yummy in the beside stand -- the big deal with a storm is for you to chart *verbally* the progress of the storm.  By "counting" after the flash to the 'boom' time after time you are seeing the progress of the storm. 

No -- they don't "count" per se, but by you watching the storm progress (wow, it's getting closer ... Hey .. it's right over us!! to "Now, it's going away!";) they begin to get the idea that you really DO understand it and are confident.  That makes it easier then for the dog to adopt your attitude. 

ALL the valerian and calms do is help calm the brain down enough so she CAN think.

And exercise?  Get creative with other forms of exercise.  Just tossing something inside over and over and over -- maybe find a dog training club locally who has indoor facilities to do some agility or flyball (whatever works).  If you have a house you may be able to make some of your own agility type equipment to use.  She may not be a "natural" at agility but anything to spur some activity.

Even doing some short spurts of "obedience" can be exercise.