What are you using to generate your gcode? There are basically two options when the gcode is generated for allowing for cutter diameter. One way is for the gcode generator to know the cutter diameter, and it generates gcode that allows for that diameter. So, the cutter path is offset round the outside of a profile, or inside a pocket, by the cutter radius. The other way is that the gcode generator creates a cutter path that is exactly on the line of the object being cut with no allowance for cutter size. What it does do is put some gcode instructions in the file that tells Mach3 (in your case) which side of the line to cut. You then tell Mach3 what the cutter size is, and it applies the offset. The advantage of doing it this way is that you don't have to regenerate the gcode if you change cutter size, or if the cutter is, say, cutting slightly over- or under-size as you can tune this out in Mach3. I use Vectric vCarve and it uses the first method; I have also used the free DXF2GCODE tool and it can do either. Important point is where you put the correction if you are cutting oversize. You say that changing tool size in Mach3 has no effect which implies that you are using the first method, so you need to change the cutter size in HSMexpress (although I don't know that software myself).

Does this make sense?