If I understand your problem correctly, your beater, dough hook etc. may be positioned too low and is scrubbing the bottom of the bowl. In your manual there is a section that shows you how to adjust whatever tool you are using so that it is positioned properly so it does not scrape the bottom of your mixing bowl. Also, make sure you have the slide along the side of your mixer in the "locked" position so the mixer is stable before you turn it on. The tool position and the unlocked versus locked feature may be causing the bumping and clunking. Hope this helps.
I don't know if this is your issue or not, but it is recommended that you adjust yours so that a dime can be in the bottom and not be disturbed when it is on. The top part is adjustable, yours might just be hitting the bottom, I would check that first. Check your owners manual on how to adjust.