There could be a few reasons for this to happen, and it's not clear from your description which reason might be the one.
The main reason might be that you have not validated your archive profile under the new archive code. I'd suggest that you clear your cache and cookies as described here, and then validate under the new code. Follow the steps EXACTLY as laid out. You will need to use the email account that you used to make the archive profile. You will get an email with a validation link sent to that address, so that is important.
It might also be that you are using search terms of three letters or less. Those do not work, unless you enclose them in quotation marks.
I am going to assume you are in the Anime archive when you are attempting to search. Each subdomain is a separate database, so you need to be in the subdomain you want to search.