Misfires (signalled by the flashing EML) can damage the catalyst.
Splutter from the exhaust may indicate that there's still a problem.
This problem then could damage the new cat as well.

Check fueling before replacing the catalyst.
One method is reading the fuel trims (especially the Long Term) with a scanner.
The Long Term Fuel Trim ideally should be around 0%.
Between 5 and 10% needs investigating, above 10% (both positive or negative) indicates a mixture problem.

How to check the cat: http://www.picoauto.com/tutorials/cat-efficiency.html