Sources said the boxes were kept in a classroom which was converted into a counting centre for the recently concluded rural elections.
The bench held that the issues raised in the petitions have been settled in an earlier matter by the high court and the decision was upheld by the Supreme Court.
Its nearest rival BJP has won 2,781 seats and is leading in 915 seats out of 63,229 seats as of 3.30 pm.
Violence rocked the July 8 rural polls, leaving 15 dead while ballot boxes were vandalised, ballot papers burnt and bombs thrown at rivals in several places.
According to police reports, 10 people have been killed so far in West Bengal in poll-related violence since the filing of nominations for the rural elections began on June 9.
On whether the clash was between two political outfits, the policeman said that the matter is under investigation and he would comment only after the investigation is complete.