I figured out the problem:
The texlive version for Ubuntu still uses pgfplots 1.8 but for the newest matlab2tikz file pgfplots 1.9 is necessary (for plots with errorbars).
It's somewhat a pain to install pgfplots 1.9 in ubuntu but after doing so it works fine again.
Maybe with the next update there could be a hint that another pgfplots version is needed.
I just love matlab2tikz, thanks for the file!
Unfortunately I have a problem with the errorbars now:
In the older version v0.4.2 points and bars were defined as (x,y)+-(xerr,yerr)... .
Now in version v0.4.4 it is (x,y) += (xerrup,yerrup) -= (xerrdown,yerrdown). It doesn't work for me to compile that file in texmaker. Did anybody have the same problem and/ or knows how to solve this?
For some reason I get errors including the tikz-file created with matlab2tikz to LateX (but other tikfiles). I use MATLAB R2012a, texmaker and ubuntu.
The problem seems to be within the table from the tikz file.
Some of the errors I get: (line with }; at the end of the table)
!Missing \endcsname inserted <to be read again>\protect}
!Extra \endcsname.\pgfutil@ifundefind..\ifx\csname#1\endcsname\relax \expandafter \pgfut...}
!use of newline doesn't match it's definition
!Argument of \@firstoftwo has an extra}