> SELECT *several_fields* FROM A, B, C WHERE *conditions* > A, B are tables with several LEFT JOINS but they act as one subquery.
You really can't expect useful help if you are going to pose questions that abstract. You have removed details that count, and made assumptions that don't necessarily hold (e.g., what does "act as one subquery" mean?)
Probably the most likely bet, on this limited information, is that there are enough base tables hidden inside your query that you're running into join_collapse_limit and/or from_collapse_limit, resulting in the planner failing to investigate the best available plan in one case. Raising those limits would help, if so. But it could easily be something else.
There's some suggestions here about how to ask useful questions: