Ok, I'm nearing the end of what cPanel support is allowed to help with and still haven't determined the issue. Here's a list of everything I've tried so far, I'll edit as needed.
- Verified low load, memory and hard disk usage
- Checked for DDOS attack
- Checked for unusual connections of any kind, especially to sql
- Optimized and repaired all databases
- Forced fsck on reboot
- Tested a website with pingdom.com, results show the DNS and connection are fairly quick but the wait period is close to 60s
- Forced cPanel update
- Upgraded MySQL to 5.5
- Rebuilt Apache with EasyApache
- Restarted server several times
I can find no reason for the database sites to be loading slowly and cPanel support staff haven't been much help yet either. I'm running out of ideas to try. Any insight would be greatly appreciated.
EDIT: Ok, I had forgotten a very important change that had been made the day before on cPanel staff's approval. I need to migrate my VMs but ran out of IPs. It was confirmed that my cPanel would run on only one nameserver and I could take the second nameserver IP for the new VM for migration purposes. It finally occurred to me that this could be the issue. Added the second nameserver back and everything is fixed.