Mapped Domain's caches not being cleared

Recently I switched from WordPress MU Domain Mapping to WPMU’s Domain Mapping Plugin for our multisite.

With WordPress MU Domain Mapping, Comet Cache was working on mapped domains and non-mapped domains.

Since switching to WPMU, the websites mapped to different domains are not having their cache files/directories being cleared when updating pages or having Comet Cache to clear said directory. The only way to clear the cache for these websites is to wipe the entire network cache, which isn’t too ideal.

Has anyone else encountered this problem with WPMU’s Domain Mapping plugin? Is there a setting I need to check?

I’d like to continue using Comet Cache, but this is sort of a big problem…