$ cat treatment2.awk

BEGIN { FS=","; OFS=","
        split("1,2,5,3,4,6,7,10,9,11,10,12,15,14,13", ORDER);
}

!T { TITLE=$1 ; T=1 ; next }

/^[ \t]*,/ { C[T++]=$2 }

/;;/ {  $0="";  T=""
        for(X in ORDER) $(ORDER[X])=" "C[X];
        $1=TITLE $1
        print
}

$ awk -f treatment2.awk data

Treatment parmeter1=value, parmeter2=value, parmeter4=value, parmeter5=value, parmeter3=value, parmeter6=value, parmeter7=value,, parmeter9=value, parmeter11=value, parmeter10=value, parmeter12=value, parmeter15=value, parmeter14=value, parmeter13=value
Treatment parmeter1=value, parmeter2=value, parmeter4=value, parmeter5=value, parmeter3=value, parmeter6=value, parmeter7=value,, parmeter9=value, parmeter11=value, parmeter10=value, parmeter12=value, parmeter15=value, parmeter14=value, parmeter13=value

$