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Make sure you are running the same GREAT version as you did previously.

The rank column is not showing consecutive numbers. What does this mean?

The rank column corresponds to the ordinal rank of the p-value compared to the p-value of other ontology terms. Output is sorted by region-based binomial p-value, so one might expect these numbers to be consecutive. However, GREAT has additional filters applied in its default display: displayed terms must also be significant by the gene-based hypergeometric test and must have a region-based fold enrichment of 2 or more. These filters may then cause some terms prioritized highly by the region-based binomial p-value alone to not be visualized.