When Chemical Registration users perform a registration using a SDFile that contains structures in V3000 molfile format, they will see that some of the compounds are registered as V2000 structures.

This is the expected behavior and Chemical Registration application will use V2000 molfile format if the structure can be represented completely with no loss of information and it will use V3000 molfile format only when required. 

In fact, according to our product teams, this behavior is not specific to Chemical Registration, but a default in most PPChem - based code, i.e., write V2000 molfiles if possible (without loss of information) and write V3000 molfiles if required.