As far as I can see, it ISN'T any different: but there are some different types of charged bolt.
There is one type that seems to include the sorceress charged bolt skill, mephisto's charged bolt, and act3 hireling's charged bolt. The hireling and sorceress share the same skill, meph's version is a little different but it seems to still use the same line for the graphics in missles.txt.
This is seperate from LEBs and lightning skeleton mages however. I'm not sure how "cast CB on hit" works but I would think that is again part of the sorc CB skill.
I tested the high and mid settings in the D2Accelerator program. In the high setting, Mephy's CBs were the usual bolts, as were sorcie charged bolts. In the medium setting, mephy shot "dots" (actually it's the quill rat spines gone transparant) as did the sorcy. I don't think I'm seeing what you describe.
If you want to get to the bottom of this, let me know exactly which options you have selected in the program (or are you using the MPQ version?)