I have come across this issue many times , and have never figured it out. It is now really bugging me with a project and I think it's about time I get to the bottom of it.
The issue is that the bevel modifier seems to only work on certain objects , and not others , without any logical reason. The image below is a perfect example....
I created a cog using the Add-Mesh-gears function , and then duplicated , giving me the two gears in the image below. I then went into edit mode and played around with them to make them visually different. Finally I added a bevel modifier to them both , and straight off the bat you can see that one works and one does not. The scales are applied to both and all the normals are correct. Changing any parameter on the bevel modifiers settings does nothing to the one that isn't working as far as I can see.
Also , interestingly enough , if you join the faulty one to the one that is working , it breaks it too.
I see no reason why one works and one does not , when they are essentially the same object just duplicated and I get this issue regularly with many objects I model working fine with the bevel modifier and some failing.
Thanks to anybody that can shed some light onto this issue.
Interestingly enough , If I add a new gear , and duplicate it , and add bevel modifiers, you can see them both working fine : 
BUT , if I go into edit mode on the green one , and add a single loopcut close to the edge as shown in orange, it sharpens up the bevels on the whole gear...... And moving the loopcut closer to the edge removes the bevels all together on the whole gear :
So I am going to assume from this experiment , that the bevel modifier bevels all of the geometry to the biggest size it can go , and if certain geometry limits it from doing so , then it shrinks the bevels on the whole object relative to that size? I'm guessing this is in some way linked to the issue I am having with bevel mods not appearing to work at all on certain objects?
Hi Matthew, I am not sure, but there is a (unfortunately hidden) setting in the Bevel Modifier, that, even when it was exposed in earlier Blender versions, tripped me up:
Clamp Overlap is On by Default!
