It is not possible to run a 32-bit MEX-file from within a 64-bit version of MATLAB. This is because MEX-files are shared libraries and it is not possible to call a 32-bit shared library from a 64-bit application (or vice versa).
To work around this issue, you will need to start the 32-bit version of MATLAB. Please note that this mode is not fully supported, but should work in most cases. You will need to have the 32-bit version of MATLAB installed for this to work. If you do have the 32-bit MATLAB installed on your 64-bit machine, you can launch the 32-bit version of MATLAB, and then call the MEX file from the command prompt.
Alternatively, if you have the source code for the MEX file, you can compile it into a 64-bit MEX file from the 64-bit version of MATLAB. To do so, you need to have a supported 64-bit compiler installed on your machine. Please refer to the following link to identify the compilers supported by the MEX interface of MATLAB R2006a on 64-bit Windows machines:
http://www.mathworks.com/support/compilers/1601_72.html#PC64