Pathik,
Would you be able to post the auto-compaction configuration for that datasource here?
The only thing that immediately occurred to me was that perhaps you are not using the default inputSegmentSizeBytes of 100 TB and that it was set smaller than the amount of data you have in a single granularity timechunk, e.g. assuming you have day granularity, inputSegmentSizeBytes is set to 1 TB and you have more than 1 TB of data in a single day. The documentation for that parameter states "Since a time chunk must be processed in its entirety, if the segments for a particular time chunk have a total size in bytes greater than this parameter, compaction will not run for that time chunk."
~Dan