Note that if a layer won't freeze, it is probably because it is the active layer. Make sure to set the layer you want to work on as active first (The first checkbox), then you should be able to freeze the other layer.

You don't have to reinstall the software. That preset is embedded in the map template, and can be regenerated from it. The preset is only needed if you need to re-apply it to the map for some reason.

To recreate the preset, start a new map using the right style, the CC3 Mike Schley Overland in this case using default settings in the new map dialog, then enter the :CC2SHEETS: dialog, make sure effects is turned on (otherwise the options are greyed out), simply hit the "New" button to create a new setting based on the current map, and name it CC3 Mike Schley.

This is a property of those symbols, standard behavior on the SS5 trees.

This setting is often configured for symbols that you may want to place along another entities, but should not go in the middle of the other entity, such as a alley of trees along a road (or in a dungeon, torches on a wall). It allows you to easily make sure all of the entities have the same distance from the centerline of the target entity.

The reason you don't see it every time you place a tree is that it is only triggered if you actually align the tree to something else. If it is placed in free empty space, there is nothing to align to, so this step will be skipped. To force this behaviour, when placing trees, move your cursor over a line/poly entity in your map, such as a road. You'll notice that once your cursor is over the center line of the road, the tree will rotate itself to align with the road ("aligning" for a tree may not be very obvious, but you'll see it rotate anyway), and if you click to place when it is in this state, you will get the Offset behavior.

If it just seems to happen out of the blue, for example in an empty area, there probably is a line or edge of a poly hidden on a sheet behind there somewhere. Even if you can't see it, CC3+ will detect it.

You can change the scaling of the fill.

If you click the FS indicator on your status bar to get to the fill style dialog, go to the bitmap files tab, and pick the relevant fill in the dropdown, you can change the values under "scaled" to change the size. Larger size means less tiling, but remember that the resolution of these fills aren't infinite, so they will appear pixelated if you set this too large.

CC3+ looks for a hex grid on the HEX/SQUARE GRID layer. Only the grid on that layer will affect the scaling/rotation/snapping of the hex symbols, and if you have more than one grid on that layer, CC3+ will pick one of them (Probably the first it encounters in the internal drawing list)

What you need to do is a little manual manipulation. Make one layer for each of the hex grids, and place the one you actually want snapping to occur for on the HEX/SQUARE grid layer.

If you ever want to place hexes on the other grids, then you need to go do a little layer renaming, renaming the current HEX/SQUARE GRID to something else, and the other layer to HEX/SQUARE GRID.