Linux SysAdmin: phpMyAdmin Bug

Description

We are a software firm, running a VPS server, with Plesk GUI. Multiple directories under httpdocs need their own install of phpMyAdmin, several of which run large databases.
We spun up a new server. Server-wide setting of php.ini defaulted max_input_var to 2,000 (/opt/plesk/php/*/etc/php.ini) and (user/local/psa/admin/config/php.ini). We know 2,000 will not be enough for our large databases. We updated all instances of php.ini to 3,000 and restarted service and server.
When max_input_var was 2,000 I could login to phpMyAdmin in a browser, without accessing via Plesk. Changing to 3,000 I get a login error. Managing this via Plesk login only, is not an option.
This is a brand new empty server. Who is to blame? The ISP is not really giving us full root access? There is a block above our level of access? The Plesk roll-out is faulty? Or will some additional config file fix this? I'm hoping for the latter. If you fix this, there may be other long-tern support work.