I know this is an older question, but for me it was something in my SQL code that is ok in a SQL Editor like SSMS or Aqua Data, but SSIS doesn't like it.

SSIS reads sql code in a single line. i.e. if you comment using -- to comment, SSIS will stop the code there and not read the rest of the code. If you comment with /**/, make sure you don't have any imbedded comments with in. (This was my recent problem.) I always comment my file name and file spec at the top of my SSIS SQL Commands. I had something like:

/*------FILE NAME

COLUMN1|COLUMN2|COLUMN3

SELECT * FROM TABLE t WHERE t.NAME LIKE '%TEST%' /*TEST RECORDS*/

------*/

The embedded comment /*TEST RECORDS*/ ran fine in my Oracle Editor, but it SSIS game me this out of sync error OP listed above. Once I changed it to:

/*------FILE NAME

COLUMN1|COLUMN2|COLUMN3

SELECT * FROM TABLE t WHERE t.NAME LIKE '%TEST%' (TEST RECORDS)

------*/

it ran without error.