The problem is in the code.
When you say
>> mysummary<-tapply(myfactor,mydata,length)
>> mysummary
you have used mydata as a factor and myfactor as the data.
tapply has (correctly) used the ordered labels in the grouping factor
(mydata) to label its output.
If you did what you probably intended:
tapply(mydata, myfactor,length)
you'll get the order you expected.
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