Guandalug,
This first thing you should do is contact The MathWorks for support. They are in the best position to give you the most up-to-date support.
That said, the Data Acquisition Toolbox is limited in its functionality. As stated in its User Manual, it can not perform buffered digital I/O. Have you tried testing your application in the Test Panels of the Measurement & Automation Explorer? If you can see your signal correctly in that utility, then it is definitely a DAQ Toolbox/MATLAB software issue. If not, then check your signal source. The data lines need a TTL signal to read data correctly.
Hope this helps.