I just answered a similar question in an email for an ALS patient. Yes, this is somewhat common after treatment. Conditions which involve loss of muscle control make tremendous amounts of tension in certain muscle segments to compensate for the loss of control. The back and legs in many cases are under lots of tension to control walking, standing, etc. which are actually quite complicated tasks that we take for granted. When you loosen these holding patterns with Shiatsu the body has to use some of the weaker muscles and rebalance the level of tension in these patterns. Over the long-term this helps to stop muscle atrophy and helps to keep connections active to parts of the body that have weakened communication from the condition. In the short-term this can cause some instability in the person for a day or so after treatment.
In my experience this is often short lived. Over the course of treatment this "side effect" very often ceases or becomes very minimal. This depends greatly on each case and the severity of the neurological/muscle damage. Personally I expect some of this for the first month to perhaps even 6 months of treatment in some severe cases, but it will eventually stop or become very minor. This incidentally also happens to less noticeable degrees in people with long term back, hip, knee, etc. issues for the same reasons. It's just less noticeable because the body adjusts faster.
How many times have you treated her? And does this happen everytime?