That definitely cost the Senate, maybe the House too.
I live in Florida, and I know how hard the 'RATS tried to shut down the military vote in the 2000 election, and since.
Do you have some particular races in mind? Assuming the uncounted ballots break 3 to 1 Republican that is only a net change of less than 30,000 votes spread across 435 Congressional races and 30+ Senate races.
I doubt these uncounted ballots would have had any major impact on the 2006 election results but they should be counted nevertheless.