Convert ciphered Roman numerals to Arabic decimals
Python 2, 415 444 440 419 416 bytes

There aren't all that many Roman numerals, after all. This script creates all of them and checks all permutations of the input, then returns the smallest match.

a=raw_input()
g=range
b=list(set(a))+[' ']*9
from itertools import*
c=[]
s={}
u=1000
for i in g(10*u):
 t,f=(10*u,9*u,5*u,4*u,u,900,500,400,100,90,50,40,10,9,5,4,1),i;r=""
 for j in g(17):k=i/t[j];r+=('W MW Q MQ M CM D CD C XC L XL X IX V IV I').split()[j]*k;i-=t[j]*k
 s[r]=f
for i in permutations(b[:9]):
 r=''
 for j in a:r+='IVXLCMQWE'[i.index(j)]
 if r in s:c+=[s[r]]
print c and min(c)or'%s failed Roman numeral test'%a