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I’m confused

Not all data was refreshed

I have two database and two jobs for refreshing data every day but on different hours.
First job runs at 8 pm (j1) and second at 5 am (j2).
From j1 I got:
lastmodifieddate: 2014-03-21 15:27:21.0000000
systemmodstamp: 2014-03-21 15:27:21.0000000
from j2:
lastmodifieddate: 2014-04-01 10:02:49.0000000
systemmodstamp: 2014-04-01 10:02:49.0000000

And this is a output data for this object (from 2014-04-01):
20:00:50: Using Schema Error Action of yes (Severity 0, state 1, error number 0, line 90)
20:00:51: Using last run time of 2014-03-31 20:01:00 (Severity 0, state 1, error number 0, line 230)
20:01:22: Indentified 1202 updated/inserted rows. (Severity 0, state 1, error number 0, line 346)
20:01:22: Indentified 0 deleted rows. (Severity 0, state 1, error number 0, line 516)

So 1202 records were updated yesterday, but almost 1900 records are not synchronised since last month (when I last time ran sf_replicate). As I understand it in correct way these records wouldn't be refreshed unless something will be changed on row and systemmodstamp will be updated, because in table exists record with bigger systemmodstamp date.

How should I manage this to exclude this issue and where is the issue?
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