The queries are complex, multiple joins to 10 plus tables, although most are to tiny enum type lookup tables. I believe it is the join between the two large tables that I have described that causes the issue, and that seems to be reflected in the different strategies in the plans. For my own learning and to clarify the problem I probably will have to try and reproduce the behavior in a test case.
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I am doing nothing to specify the optimizer. Do I have configurable options in that regard? I was unaware of them.
