This can be the result of several issues which cannot be understood from your description.
First, the VMD plugin is a geometry based algorithm, depending on the O---H-X distance and angle. These parameters are dependent on the force-field used and on you loading the proper connectivity and selection keywords. VMD only considers a bonded hydrogen.
Second, there are also energy based methods based on MO, e.g.:
Article Systematic Detection and Characterization of Hydrogen Bondin...