using make to run binaries

[Andreas Maunz]

Hi, we use 'make' primarily for compilation of C++ code using g++ under Linux. 
Working in a scientific environment we constantly need to test our programs on 
some
data. As we found 'make' to be a convenient utility we use it not
only for compilation of the binaries but also for running test cycles on
our data, i.e., we use it to launch our binary, somehow like that:
# make test.data
which then constructs a command line like this
# /path/to/binary [args] > test.data
The problem is that the output in 'test.data' differs from the output obtained 
by running the very same command line manually.
Anybody got an idea what might be the reason? Isn't 'make' suitable for
running executables?
Regards, Andreas