Getting the same problem with same message on multiple machines and multiple users, all using Chrome on Windows and Ubuntu. The solution above doesn't work.
In Options, Filter Lists:
Adblock Warning Removal List already has Enabled unchecked, but the setting is not respected.
Also if the pop-up is dismissed, it comes back for the same site on page refresh. E.g. when browsing gmail, shows on first page load. Dismiss. Click into an email to read, pop-up shows again.
For some users it re-occurs for every click on gmail
Definitely seems like a bug.
The only way to avoid is to disable adblock for that site.