Some databases not getting backed up through the job - sql

I am getting this weird problem with my backup job.
I have more than 1000 DB's on my SQL server stack. There is a weekly and daily backup jobs set to take the backup. Weekly jobs runs on every sunday and does the full backup and then the daily job does the differential backup.
Now I realized that the last Full backup of some of the databases is not updated.
I checked the job history and the job was successful without any error. When I check in the backup folder, the timing of the backup seems a bit doubtful e.g
26/10/2014 23:34 2,759,240,192 DB1 2014-10-26 23.19.59 Full.bak
26/10/2014 23:36 319,891,968 DB2 2014-10-26 23.34.46 Full.bak
26/10/2014 23:36 160,771,072 DB3 2014-10-26 23.36.17 Full.bak
26/10/2014 23:48 3,505,426,944 DB4 2014-10-26 23.36.59 Full.bak
27/10/2014 00:03 4,322,182,144 DB5 2014-10-26 23.48.12 Full.bak
***27/10/2014 00:25 7,266,648,576 DB6 2014-10-27 00.04.13 Full.bak
27/10/2014 03:31 67,190,649,344 DB7 2014-10-27 00.25.51 Full.bak***
27/10/2014 03:32 270,017,024 DB8 2014-10-27 03.31.19 Full.bak
There are some replication job runs at around 2 O'clock. I thought that may be the problem and I changed the time for my differential backup job a bit early so that it finishes before the replication job starts.
But the result is same . Job is successful. but most of the backups did not get updated and this time the last backup was taken at 19:36 and after that no backup at all.
Its really critical,Can someone please help me with what can be the reason for this ?
Your help is much appreciated.
I am using SQL server 2012
Thanks

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GO
hurray a working answer.
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