New update of Domain Mapping crashed my server

The latest version of Domain Mapping caused all my mapped domains to be "invalid." I tried to refresh the mapping, but it remained invalid. Then, my server got shut down for overusage because I believe the plugin script was continuously running. Once I deactivated the plugin, I could get my server working again.

Trouble shooting: I noticed that under the public_html folder, I have the normal wp-content, where all the plugins reside. However, I also noticed that there is another plugins folder directly under public_html (not in any wp-content folder). In that second plugins folder there are some of the installed plugins, but not all of them. The domain mapping plugin is also found in the plugins folder.

I'm not sure how this second plugins folder got there, but I'm wonder is this might be the conflict since it is duplicating the other main plugins folder with domain mapping in the main wp-content folder. I renamed that extra domain mapping file and that seem to help my server get back online. Maybe that extra domain mapping plugin was running a script open-ended??

So now, I would like to get domain mapping working again, but I'm afraid of another shutdown. It's not possible to activate this plugin on a site by site basis, right?

Any suggestions? Completely delete the domain mapping plugin and re-install it? Right now, it is only deactivated. I did go through the deactivate/reactivate process and that didn't help.

Thanks, Joe.