Despite some time spent bisecting the Fisheye source tree I haven't been able to identify the exact commit that is responsible, but I have identified that this issue was first introduced in Fisheye 3.1.

The problem

The P4Scanner.indexRevisions method builds up a list of changesets until the list is larger than the batch size. It then passes them off to the indexBatch() method. Since 3.1 the list is not cleared after the batch is indexed and so all changesets that have been indexed so far are re-passed to the indexBatch method