Short answer:
Section 102.112 of Florida law requires that all counties file their returns with the State by 5pm on November 14.  However, it states that she can accept late returns although it does not state under what circumstances she can accept or refuse to accept late filings.  Florida also allows manual  recounts to begin up to and on that same day under Section 102.166.  Bush's lawyers argue that 102.112 must be read in statutory isolation as an immutable deadline beyond which other provisions of the statute that require counting after this deadline are exercises in futility.  Gore's lawyers argue that these are two separate provisions that have to be read together to determine how long votes can be counted; essentially they feel that 102.166 is essentially an overtime provision.  Ironically, it was Gore's lawyers who argued that the 102.168 contest provision had to be read in statutory isolation as a justification for any court remedy for resolving a contested election, even beyond those outlined in the statute.  Bush's lawyers argued that 102.168 had to be read in a way that was congruent with the remaining statutory provisions.

Long answer:
There is a statutory conflict between the timeline for filing returns with the State under 102.112 and the manual recount provisions under 102.166.

102.112  (1) Returns must be filed by 5 p.m. on the 7th day following the first primary and general election...If the returns are
not received by the department by the time specified, such returns may be ignored and the results on file at that time may be
certified by the department.

102.166 (4)(a)  Any candidate whose name appeared on the ballot... may file a written request with the county canvassing board for a manual recount....(b)  Such request must be filed with the canvassing board prior to the time the canvassing board certifies the results for the office being protested or within 72 hours after midnight of the date the election was held, whichever occurs later.

As you can see, Section 102.166 allows for the manual recount process to begin up until the day the county certifies its
returns to the state.  However, Section 102.112 requires that counties submit said returns by 5pm 7 days after the election.
Returns can be filed after this time, but the Secretary of State may choose to ignore them (she does not have to).  These two
statutory provisions conflict.  If we are to believe Bush's campaign manager, Florida law forces her to certify the counties
returns on Nov 14 and ignore late returns even though the law both allows her to accept late returns and allows for a manual
recount process to begin on Nov. 14, a process that may eventually force the county to do a manual recount of every ballot.
Clearly, a county could not start the legally permissible manual recount process outlined in Section 102.166 on the day that
returns are due under 102.112 and be finished that same day.

The primary role of the executive branch is the enforcement of all the legislative branch's statutes.  As an executive officer, the
Secretary of State has a legal obligation to enforce every aspect of Florida's election code, not just the ones that improve her
candidate's chances for victory.  In the course of exercising the discretionary authority granted her by one section of a statute (in this case 102.112), she can not forego her obligation to enforce other sections of that same statute such as 102.166 (or any
other statute for that matter).  In other words, the executive branch's ability to interpret law and exercise discretion can not
render obsolete or ignore other legislative provisions -- executives do not have that power because their foremost duty is to
enforce all the laws; any interpretive and discretionary power is subordinate to that enforcement mandate.