The SelectByProperty function allows you to select objects at every level of the Molecular Data Model hierarchy. Using this API you can actually create selections which are not feasible from the Selection commands in the GUI.
For example, if you use:

\$object->SelectByProperty('Molecule Name MYMOL');

it will select the molecule MYMOL but none of its children (i.e. none of its chains, residues or atoms).

The attached script illustrates how this issue can cause discrepancies when using SelectByRadius after SelectByProperty.

If SelectByProperty only selects a residue and not its underlying atoms, it is as if only the center of that residue is selected therefore the subsequent SelectByRadius function will select fewer surrounding amino acids. This is evident by the two print statements which report the number of selected residues (first when the MTX atoms are not selected and then when they are selected).

Therefore, to avoid this discrepancy, be sure to include an Atom-level specification in the SelectByProperty statement.