Sounds like the new battery is the problem...maybe a dead cell or something. The top mechanism requires a considerable amount of current to operate. You may have to bench test the battery. Also make sure you operate the top with the engine running, not just the ignition key turned on.
2009 ML350 (84K) - Family vehicle
2001 CLK430 Cabriolet (71K) - Wife's car
2005 BMW 645CI (124K) - My daily driver
2012 Mustang V6 (60K) - Daughter's car