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Just to clarify.
You have one U3S kit, built with the LPF relay board, and with the PA unit inline between the U3S and the LPF, and another U3s kit built as a single band but also using a PA?
That you see an output power difference between the two kits, multiband kit with the 10m filter in slot 1 and the single band kit?
Or are you comparing the same U2s kit with and without the LPF in place? If so, are you correctly putting the PA between the U3S and the LPF relay board? If not, do you have the appropriate LPF between the PA and the antenna?
Are you using the same physical 10m LPF filter to do the comparison?
Is there a difference in the power draw by the U3S between the two configurations?
If it's a comparison between a single band U3s and a multiband U3s, it could entirely be down to construction and component differences between the kits.
Always fun trying to troubleshoot things like this, but a better understanding of the current setup is needed.