Two jobs updating the same table

Job 1 comprises of transformation #1 and transformation 2.

Transformation #1 reads from a .csv file of format label, description and updates Table 1 which has
var_id, label, description, src_id.
Transformation #2 reads the source string from .csv file #2, does a lookup and updates src_id(=1) (for source 1 say). ((.csv input->databaselookup->insert/update)

Job 1 comprises of transformation #1 and transformation 2.

Transformation #1 reads from a .csv file of format label, description and updates Table 1 which has
var_id, label, description, src_id. (same as above)
Transformation #2 reads the source string from .csv file #3, does a lookup and updates src_id(=2) (for source 2 say). ((.csv input->databaselookup->insert/update)

However, when I run the above two jobs, the first set of inserts works fine. The second set creates problems.

I want:
label1, desc1, 1
label2, desc2, 1
....
label1, desc1, 2,
label2, desc2, 2

But I get
label1, desc1, 2
label2, desc2, 2
....
label1, desc1, 2,
label2, desc2, 2

How do I go about it?