reading file with missing values in python pandas

What version of pandas are you on? Interpreting empty string as NaN is the default behavior for pandas and seem to parse the empty strings fine in your data snippet both in v0.7.3 and current master without using the na_values parameter at all.

In [10]: data = """\
10/08/2012,12:10:10,name1,0.81,4.02,50;18.5701400N,4;07.7693770E,7.92,10.50,0.0106,4.30,0.0301
10/08/2012,12:10:11,name2,,,,,10.87,1.40,0.0099,9.70,0.0686
"""

In [11]: read_csv(StringIO(data), header=None).T
Out[11]: 
                   0           1
X.1       10/08/2012  10/08/2012
X.2         12:10:10    12:10:11
X.3            name1       name2
X.4             0.81         NaN
X.5             4.02         NaN
X.6   50;18.5701400N         NaN
X.7    4;07.7693770E         NaN
X.8             7.92       10.87
X.9             10.5         1.4
X.10          0.0106      0.0099
X.11             4.3         9.7
X.12          0.0301      0.0686

The parameter na_values must be "list like" (see this answer).

A string is "list like" so:

na_values='abc' # would transform the letters 'a', 'b' and 'c' each into `nan`
# is equivalent to
na_values=['a','b','c']

Similarly:

na_values=''
# is equivalent to
na_values=[] # and this is not what you want!

This means that you need to use na_values=[''].