Opening a case is the correct thing to do in cases like this. You should never see messages like that and they'll be able to help determine what's going on. What you're trying to do should work without issue.
One thing you can check is whether you've hit your limits on custom fields. If you have, then you'll run into issues with case insensitive ...
There is no email limit from Apex. The limit is on the number of times the sendEmail() method can be invoked from Apex. You need to ensure that you're not calling the sendEmail() method inside a for loop.
Figured out the issue. I didn't test by sending and replying to the Proxy email designated in the email-to-case setting. It also requires the setting of including the thread ID in the subject or body also located in the Email-to-case setting.