Dear Jenn,
Yes, a side effect of stimulant medications (like Ritalin and Dexedrine) can be emotional lability, sensitivity, crying. It was a good idea to start him up again on the medication before school actually starts, so his body can adjust to it.
Sometimes, if children cry easily as a side effect of stimulant meds, and they are taking the short-acting form, they will be more stable on the longer acting forms (such as Ritalin SR or Dexedrine spansules). No change is really indicated at this point. Give him time to adjust, and see if the effect wanes (if indeed it is due to the medication).
You probably needn't worry about the long-term problems you mentioned. There's no indication, after many years of experience with the stimulant medications, that they result in the kinds of difficulties you mentioned.