hi welcome to health care magic!
It is possible that your mother is suffering from 2 conditions.i.e. joint/muscle pain
in addition to the thyroid disease
for which she is getting treatment.I would like to know your mothers age,You have not mentioned which joints are involved and at what time of the day she gets more pain and whether she is likely to be suffering from any vitamin deficiencies
You may consider the following investigations1)complete blood count2)rheumatoid factor3)ana
in case any of these investigations are abnormal you may consult your physician for further investigations and treatment.Also consider a multivitamin
hope this helps!