Allow me to introduce myself. I am the development lead for SiteAdvisor. I have been made aware of the threads regarding the toolbar placement of the new version of SA. I have escalated these threads to management.
As a work around for the problem with placement of the SA toolbar, you can suggest to users to place the SA button to the left of other toolbars instead of to the right. I have attached an example below. (click the thumbnail below)
I cannot make any promises but I can assure you engineering is looking into this issue.