Base Peak Intensity different than higher value in Mass Intensity Map
One possibility for the discrepancy is that different peak centroiding / integration algorithms were used at different stages in the data.

For example, the base peak intensity recorded in the plain-text (uncompressed) scan data is probably calculated by the instrument in real-time during acquisition.  The intensities of all detected peaks are also recorded by the instrument, of course, but those intensities may be affected by processes such as centroiding that are not applied to the plain-text recorded base peak intensity.

An exact answer to your question will depend on many factors, such as whether spectra were recorded in profile mode or centroid mode, whether spectra were compressed during conversion to mzXML format, and also details of the (possible) centroiding algorithms and BPC algorithms used by the instrument firmware during data acquistion.  (Good luck trying to find the exact code for vendor firmware...it's probably proprietary.)