pd.DataFrame.update very long in 0.20 compare to 0.19.2
Same dataFrame, left: empty dataframe, right: full of zero (6000 x 6000 each) with a 3 level multiindex:

```python
# with 0.19.2
%timeit test.update(A)
1 loop, best of 3: 7.85 s per loop

# with 0.20
%timeit test.update(A)
1 loop, best of 3: 3min 25s per loop

```
#### Problem description
The update function in pandas 0.20 is much more longer with the same data and same routine.

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

<details>
# 0.20
INSTALLED VERSIONS
------------------
commit: None
python: 3.6.0.final.0
python-bits: 64
OS: Darwin
OS-release: 15.6.0
machine: x86_64
processor: i386
byteorder: little
LC_ALL: None
LANG: fr_FR.UTF-8
LOCALE: fr_FR.UTF-8

pandas: 0.20.1
pytest: 3.0.5
pip: 9.0.1
setuptools: 27.2.0
Cython: 0.25.2
numpy: 1.12.1
scipy: 0.19.0
xarray: None
IPython: 5.1.0
sphinx: 1.5.1
patsy: 0.4.1
dateutil: 2.6.0
pytz: 2017.2
blosc: None
bottleneck: 1.2.0
tables: 3.3.0
numexpr: 2.6.1
feather: None
matplotlib: 2.0.0
openpyxl: 2.4.1
xlrd: 1.0.0
xlwt: 1.2.0
xlsxwriter: 0.9.6
lxml: 3.7.2
bs4: 4.5.3
html5lib: None
sqlalchemy: 1.1.5
pymysql: None
psycopg2: None
jinja2: 2.9.4
s3fs: None
pandas_gbq: None
pandas_datareader: None

</details>

<details>
# 0.19.2
INSTALLED VERSIONS
------------------
commit: None
python: 3.6.0.final.0
python-bits: 64
OS: Darwin
OS-release: 15.6.0
machine: x86_64
processor: i386
byteorder: little
LC_ALL: None
LANG: fr_FR.UTF-8
LOCALE: fr_FR.UTF-8

pandas: 0.19.2
nose: 1.3.7
pip: 9.0.1
setuptools: 27.2.0
Cython: 0.25.2
numpy: 1.12.1
scipy: 0.19.0
statsmodels: None
xarray: None
IPython: 5.1.0
sphinx: 1.5.1
patsy: 0.4.1
dateutil: 2.6.0
pytz: 2017.2
blosc: None
bottleneck: 1.2.0
tables: 3.3.0
numexpr: 2.6.1
matplotlib: 2.0.0
openpyxl: 2.4.1
xlrd: 1.0.0
xlwt: 1.2.0
xlsxwriter: 0.9.6
lxml: 3.7.2
bs4: 4.5.3
html5lib: None
httplib2: None
apiclient: None
sqlalchemy: 1.1.5
pymysql: None
psycopg2: None
jinja2: 2.9.4
boto: 2.45.0
pandas_datareader: None

</details>



