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It is possible in VSCode to have multiple repositories opened at once.
The "Generate Commit Message" will only generate a commit message for the first (top, on the sidebar) repo, ignoring the rest. If ran again, it will say there are no further changes, unless the first repo in the list (top) is first closed.
Above: The 1st repo correctly has a message generated, while the 2nd does not, despite having modifications.
Above: Rerunning "Generate commit message" after changes have been committed to the first repo results in the message "git diff is empty", despite modifications existing in repo 2.
Above: If repo 1 is first closed, then running "Generate Commit Message" detects the changes to repo 2 and a commit message is generated.