Converting a large SQL Server database to MySQL. Database corruption? Can't access data after transferring
As you have a dedicated server, there is no reason not to use native MySQL command to issue queries directly. Avoiding phpMyAdmin means avoiding one more layer between you and database while trying to figure out what went wrong.
My first thought is - are you actually trying "select * from table" on a 45 million row table? That could cause all kinds of problems.

1) Try "select count(*) from table" first. See if you get 0 or 45M.

2) See if partition with your data is large enough. Yes, this kind of omission happens.

3) Try using MyISAM instead of InnoDB to reveal possible server misconfiguration issue.

Perhaps it makes sense to use our battle-proven commercial database migration tool Full Convert Enterprise for your data conversion? It runs on Windows only, though. Quickest path