Do you have an IDENTITY column as the PK of your fact table? If so, use that to drive your looping and remove the TOP (100000)

UPDATE ...

What is the primary key on table MVF_Transport_Acc?

Try running this

CREATE TABLE #FileData
(
  RowNo   INT   IDENTITY(1, 1) PRIMARY KEY NOT NULL
, FileRowID CHAR(2)  NOT NULL
, FileRowData VARCHAR(20) NULL
, GroupID  INT   NULL
);

You need to use a technique which maintains the physical order of the rows in the file in order to be able to add any sort of grouping identifier.
The...