I haven't been able to figure this out totally because it's not happening for every one of my test employees -- however one customer on 4.3.0.23 had it occur on all her employees and I can duplicate it on some employees in my test 4.50 system.
For employees with CT withholding codes
If the period ending date in payroll data entry is in 2011 and the current payroll quarter is in 2012 -- when you go to run the payroll tax calculation you may notice that some CT employees have no CT tax withheld unless they have an override amount in their employee maintenance screen.
I was able to resolve this by changing the period end date so it falls into 2012 and recomputing the payroll taxes.
