Search response issues when upgrading from 0.90.13 to 1.4.2

Hi guys,

I am facing some issues while upgrading from ES 0.90.13 to ES 1.4.2.
I think I might be doing something wrong in forming queries/filters.

With both the versions I am executing following query:
curl -XGET '' -d '{"fields":["hits"], "query":{"filtered":{"query":{"match_all":{}},"filter": {"missing": {"field": "entry_ids" }}}}}'

But strangely, I am getting different responses from different versions.
The number of hits also differ for different versions.

I have checked the data is indexed for both the versions and all data exists.
I have gone through the Breaking changes doc, but can't find what causes this issue.

The difference in response is driving me nuts :weary:.
Can someone help on fixing this issue, Do I need to make some changes in settings/mappings for the new version?