Minecraft 1.10.2
Forge 12.18.3.2422
BetterBuildersWands-1.10.2-0.11.1.220
minecolonies-universal-1.10.2-0.8.3690

Building Tool and Scan Tool conflict with builder wands. Maybe flip the recipe 180° (flip it up-side-down)
ModList:
https://pastebin.com/XZWj3KEF

Current recipes:
recipes.addShaped(minecolonies:scepterSteel, [[null, null, minecraft:iron_ingot], [null, ore:stickWood, null], [ore:stickWood, null, null]]);
recipes.addShaped(minecolonies:scepterGold, [[null, null, ore:cobblestone], [null, ore:stickWood, null], [ore:stickWood, null, null]]);

Proposed change:

recipes.addShaped(minecolonies:scepterSteel, [[null, null, ore:stickWood], [null, ore:stickWood, null], [minecraft:iron_ingot, null, null]]);
recipes.addShaped(minecolonies:scepterGold, [[null, null, ore:stickWood], [null, ore:stickWood, null], [ore:cobblestone, null, null]]);

Source Change(I think, I can make a pull request if you wish):

minecolonies/src/main/java/com/minecolonies/coremod/util/RecipeHandler.java

   //Register Scepters
    GameRegistry.addRecipe(new ShapedOreRecipe(new ItemStack(ModItems.scanTool, 1), "  S", " S ", "I  ", 'I', Items.IRON_INGOT, 'S', WOODEN_STICK));
    GameRegistry.addRecipe(new ShapedOreRecipe(new ItemStack(ModItems.buildTool, 1), "  S", " S ", "C  ", 'C', "cobblestone", 'S', WOODEN_STICK));

As far as i can see you have forestry in your modlist. It should be possible to switch betwenn the recipes in the forestry worktable.

True, I also have MineTweaker. However I'm thinking of other people that don't know how to use minetweaker and/or don't have Forestry and Better Builder's Wands has become very popular.

It a quite common recipe however you turn it.
I think the best idea would be making a button in the townhall to get it for free

Yeah I thought for a while we probably should change that, will think of something good.