So, TALtech's File-Wedge may work for you. It could potentially capture the serial input, filter it, and write the appropriate fields into the database file.
(it does have some fairly advanced filtering)
Or, write a VB program to capture the serial input, parse it, and write to the DB file yourself.
What does the current software do? Does it currently read the serial input?
Would the data capture program be required to interface to the existing software? (I'm not sure that a windows program can easily (if at all) automate a DOS based app...)