APR verifications ALWAYS require 3 steps:
1. Manually recheck the AF to be sure the right amount of PPFCs have been deducted.
2. Verify the payment schedule - preferably by running dollars and dates through a spreadsheet that simulates your servicing environment.
3. Enter the numbers and run the APR verification program.
Step 1 will catch errors in classifying fees as FCs--sometimes these errors are intentional. Step 2 will catch problems with PMI premiums & termination, teaser rates and other payment irregularities--sometimes these problems are due to faulty software or settings. Step 3 is least likely to find problems, but you've gotten this far so you might as well do it.