SSIS -> Flat File Connection Manager -> Preview -> Data Rows To Skip gets evaluated at design time and at runtime. This is confusing since this feature refers to ‘Preview’ of the data and is not expected to be evaluated at runtime. Unfortunately this causes issues in production since data is skipped based on this setting at runtime.
Two potential resolutions:
1) (Preferred) Change the behavior so that it is only evaluated at design time.
2) Clarify in the user interface that this feature is evaluated at both design time and runtime.
There are two separate features which are potentially used to skip rows. The first feature is the ‘Column names in the first data row’ is shown on the SSIS -> Flat File Connection Manager -> General tab. The second feature ‘Header rows to skip’ is on the same tab. It would seems that these features meet the need for runtime skip of the data.