The LCN column should have the LCN value for the freq in it.
Just because you enter the freq into #1 in the software, doesn't mean that an LCN of 1 has been programmed.
I think most of my systems are programmed like the example on the left, where the # of the position also matches the value entered into the LCN column.
Sometimes when trying to figure out a system not listed on RR (especailly an LTR system) I will edit the LCN's to different values during the process of figuring out repeater numbers and end up with something that tracks correctly, but looks like the example on the right where the # and the LCN do not match.
If you are used to the Win96 or Win97 (and other) software where the memory channel number determines the LCN, this software doesn't work like that.