I have strange behavior with a APEX Batch job

I run this job with batch size of 1 and it puts a job of 1000 Batches to process. However after it run for some time I have seen following behavior

1. I see the batches are processing fine say like it has processed 300. All of a sudden I see all jobs completed and it says it processed 800 batches (not sure where the other 200 batches go). Looking at the data looks like it did not process everything that should have been processed.

2. Some times I see it is processing fine say at 400th batch and all of a sudden it would say completed with all 1000 batch completed. Looking at the data looks like it did not process everything that should have been processed.

Any ideas why this could happen ?

The batch class internally call another class method in the execute method. This method has some what more logic in it. However this method when run individually does not have any issues (No Heap size issue or other performance issues).  Not sure because of the call method the complete Batch job is abruptly aborted. (with specifying any error)

I have opened a case with Salesforce but want to see if any one else have seen this issue.