Since the MWE was not available, I took the liberty to study you recent post your example, follow your concern, and this is what this attempt has done for a possible solution to your question.
When scale ticks={base 10:-3} key is used, the base 10:-3 will divide every tick label by 10^-3, resulting in a common factor 10^3 for y axis and causing problems on number formatting. A quick fix is to remove the fixed style in the style.
I use your example to demonstrate the idea.

Code:
\documentclass[]{article}
\usepackage{tikz}
\usepackage{pgfplots}
\begin{document}
\begin{tikzpicture}
\begin{axis}[%
width=\textwidth-\widthof{100},
height=8cm,
xmin=0,
xmax=0.04,
xlabel={[S]=$\frac{\texttt{mol}}{\texttt{L}}$},
xmajorgrids, scaled x ticks = false,
x tick label style={
/pgf/number format/.cd,
fixed,
precision=3,
/tikz/.cd
},
ymin=0,
ymax=0.23,
ylabel={[V]%\textsubscript{0}]=$\frac{\texttt{mol}}{\texttt{L} \cdot \texttt{s}}$
},
ymajorgrids,scaled y ticks={base 10:-3},
%/pgf/number format/sci subscript, % alternative expression (method 2)
y tick label style={
/pgf/number format/.cd,
%fixed, % mark out this style (method 1)
precision=2,
/tikz/.cd
},
legend style={at={(0,1)},anchor=north west}
]
\addplot [
%color=mycolor1,
mark size=2pt,
only marks,
mark=diamond*,
mark options={solid,}%fill=mycolor1}
]
table[row sep=crcr]{
0.001198562 0.0344717664736108 \\
0.002394254 0.0365895792303057 \\
0.003984064 0.0563386501133353 \\
0.011857708 0.111166458313178 \\
0.019607843 0.164120742512085 \\
0.031007752 0.220381981506325 \\
0.038461538 0.22523224268105 \\
};
%\addlegendentry{};
\end{axis}
\end{tikzpicture}
\end{document}
– idkfa Jan 14 '14 at 22:09scale ticks below exponent={-3},%fixed,for x and yprecision=1,for x and y Maybe you see now what I meant. Also in your plot the label is within the axis label. Anyway thank you for your help, since your input to comment fixed out lead to my solution! If you have any other input on how I can achieve that differently / easier I'm willing to learn!precision=1for0.01to force1 * 10^-2instead of usingprecision=2to keep0.01. Did I get you right? – idkfa Jan 14 '14 at 23:33fixedfor number format, then adjust the precision according to your data. If you mark out thefixedfor x-axis, base 10 notation comes out. If the layout is jammed with digits then usesci subscript(method 2). – Jesse Jan 14 '14 at 23:51