New to Leica Controllers

It depends, the data collector has to project a XY system somehow, how Leica does it and how you TOLD it to do it is impossible to say without seeing what happened.

There should be an option to review an inverse between two points and see the grid vs. ground values, you will want them to match within a few ppm's.

If they are out more than say 20ppm, I would consider changing my scale factor. That would be 9999.80' in 10,000.00'. You need to know what that value really is on your job if you wish to be comfortable with what is happening. Running a scale factor of 1 in some routines means you are just using the existing projection along the ellipsoid and with the grid scale factor also applied, depending on your location you could be quite a bit from ground.

Each 20' in elevation creates 1 ppm, and where you are in the grid creates an additional scale value.

Are you on a local project coordinate system (e.g. 5000, 5000, 100), or using GNSS coordinates projected to your respective state plane coordinate system? In my experience, for projects with assumed coordinates, you should set your scale factor to 1. This way all TPS measurements are not scaled, and all measurements are GROUND distance as measured by the EDM. This is a good assumption on planimetric surveys where the world can be assumed flat due to the "small" project size.

However, if you are going to use GNSS on the state plane grid I would recommend using a scale factor provided by the data collector for where you are on the coordinate grid. By memory, on Lica Viva collectors (captivate should be the same) I use the Station Coordinate and Height scale factor option under TPS Scale in the Job Properties menu. This provides a data collector software generated combined scale factor to scale the EDM measurements accordingly so that all coordinates are on the SPC grid for each setup that you make. This way, conventional traverse will tie between GNSS control points. I find it best to use all ground or all grid coordinates for a project. EDM set on GNSS control with a scale factor of 1 will shoot ground distance from grid coordinates - not an apples to apples comparison and they will not tie on a long traverse!

In short, my advice is:
If you are on assumed ground coordinates, stay on ground. Use a scale factor of 1.00000000
If you are on SPC grid, use the collector provided scale factor for station coordinate and height. Check the factor with CORPSCON if you feel the need to.