Can you be more specific when you say it sounds completely different? If your presets are routed in parallel and one of them is a Thru preset, that is essentially create a separate dry path, so it should sound different than Flanger + Thru in series (in parallel, there will now be a lot more of the dry signal). If you turn Kill Dry on and bypass the Thru preset in parallel, that should sound more similar to the series routing.