Understanding results of an energy audit
Plugging air leaks in you home is a bit like sticking fingers into a leaking dyke. Plug one hole and another one breaks through. Generally, the situation should have improved with new windows and doors (if installed properly).

The technician doing the post-audit should have identified where the air was coming from so you could fix that too.

One possibility is that a fire place flue or external fresh air duct to your funrnace was open during the blower test. This would have let a huge amount of air in. Other things to look for are stuck flapper valves in bathroom and kitchen vents.

Another place to check and seal would be around the sill plate. Often there are a number of small air leaks here. Individually they are not large but in sum they can amount to a significant air leak.