The maximum number of matches refers to the estimated maximum number of matches that a function should produce. This value is used to determine the ranges of values allowed in the function dialogue boxes, eg the lowest "minimum score" for the "find similar spans" function ( see section Find similar spans). Altering this value will in turn alter the range of values available in a function.
The maximum number of matches is altered using the Options menu. This only provides a guideline. The function itself will always attempt to calculate ALL the matches but this may result in an "out of memory" error for large numbers of matches. For very large numbers of matches, the function will also be very slow.