DTS Type Mismatch at Join
Ok. I was able to find the root cause (hopefully) and circumvent it. Most likely the reason was type mismatch 'join' was because ACCT_ID was NULL in the source table.

The below worked fine:

IF NOT isNULL(DTSSource("ACCT_ID"))
    varamt = Lookup ("Lookup_tbl1",
        [Lookup_tbl1].[Amount],
        Array(DTSSource("DEPT_ID"), DTSSource("ACCT_ID")))
    IF (NOT isEmpty(varamt) or NOT isNULL(varamt)) or varamt&lt;&gt;"" THEN
        DTSDestination("AMOUNT") = varamt
    ELSE
        DTSDestination("AMOUNT") = DTSSource("AMOUNT")
    END IF
ELSE
    DTSDestination("AMOUNT") = DTSSource("AMOUNT")
END IF