Whilst the 2000 election was a sweep for the PPD, Netting them the Governorship, both chambers of the legislatures and a majority of Mayoralties from the PNP - they did end up losing one aspect of the elections on the island: the combined party vote for the At-Large Senators
Whilst they won the senate when you account for the district seats - losing the At-large vote resulted in them tying in the Regular 11 seats at 5 PPD 5 PNP 1 PIP (With an additional senator given to the PNP to account for the fact that they were now a superminority in the Senate
Furthermore, this election is emblematic of the modern strength that the PNP has in the Puerto Rico senate - with it being the chamber that they're stronger in and is easier for them to win.