df.stack() still misbehaving in unsorted case
Migrating from the comment [here](https://github.com/pandas-dev/pandas/issues/16323#issuecomment-315397947), we still have as of 0.20.3 and current master that

#### Code Sample
```python

import pandas as pd

# We create a MultiIndex
PAE = ['ITA', 'FRA']
VAR = ['A1', 'A2']
TYP = ['CRT', 'DBT', 'NET']
MI = pd.MultiIndex.from_product([PAE, VAR, TYP], names=['PAE', 'VAR', 'TYP'])

# We create a dataframe with multindex MI
V = list(range(len(MI)))
DF = pd.DataFrame(data=V, index=MI, columns=['VALUE'])

# We unstack the dataframe and drop level 0
DF = DF.unstack(['VAR', 'TYP'])
DF.columns = DF.columns.droplevel(0)
DF.loc[:, ('A0', 'NET')] = 9999

# We stack the dataframe
DF0 = DF.stack(['VAR', 'TYP'])
# DF0 is wrong
DF1 = DF.sort_index(axis=1).stack(['VAR', 'TYP'])
# DF1 is right 

print(DF0.sort_index())
print(DF1.sort_index())
print((DF0.loc[DF1.index] == DF1).all())
```

gives two different frames which don't match.

#### Problem description

The association between index, column coordinate, and value shouldn't break just because of lexsorting.

#### Expected Output

Matching values, and True.

#### Output of ``pd.show_versions()``

<details>
INSTALLED VERSIONS
------------------
commit: None
python: 3.6.1.final.0
python-bits: 64
OS: Linux
OS-release: 4.4.0-83-generic
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: en_CA.UTF-8
LOCALE: en_CA.UTF-8

pandas: 0.20.3
pytest: 3.1.2
pip: 9.0.1
setuptools: 27.2.0
Cython: 0.25.2
numpy: 1.12.1
scipy: 0.19.1
xarray: 0.9.6
IPython: 6.1.0
sphinx: 1.6.2
patsy: 0.4.1
dateutil: 2.6.0
pytz: 2017.2
blosc: None
bottleneck: 1.2.1
tables: 3.3.0
numexpr: 2.6.2
feather: None
matplotlib: 2.0.2
openpyxl: 2.4.7
xlrd: 1.0.0
xlwt: 1.2.0
xlsxwriter: 0.9.6
lxml: 3.6.0
bs4: 4.6.0
html5lib: 0.999
sqlalchemy: 1.1.11
pymysql: None
psycopg2: 2.7.1 (dt dec pq3 ext lo64)
jinja2: 2.9.6
s3fs: None
pandas_gbq: None
pandas_datareader: 0.4.0

</details>
