Sounds like the data in the file isn't completely loaded into table1 before you start the insert into table2, maybe getting dirty reads... what isolation level? I'm going to assume that table1 is a staging table and table2 is the prod table? If not why not just use multicast task to load both table at the same time from the source file...

maybe explicitly start a transaction around the first task of loading table1 or put a pause between loading table1 to inserting table2...