I have this problem as well. This is for at least 2 projects and 2 users trying to update them. A new swimlane on board A will only appear if it's in the 1st or 2nd position, but not the 3rd. A new swimlane on board B will only appear if its in the 1st position, but not the 2nd or 3rd.
A swimlane will display only if there are issues that match its filter and only if those issues are not displayed in a higher ordered swimlane.
If that doesn't address your question please provide more details about the definitions of your swimlanes and examples of the issues displayed in them when they are ordered in different ways.
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