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WHMCS slow time to first byte

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I'm having some issues with my WHMCS pages where the time to first byte is very long compared to the rest of my website.

We run Joomla on our site and the time to first byte for Joomla is 0.2-0.3 sec when testing from a server within Europe.

However when we test any WHMCS pages on the same server with the same apache and PHP config we get time to first byte times of 4-5 seconds...
This only happens to the WHMCS .php files.

I've already switched from using PHPwincache to PHP Opcache (also known as zend optimizer plus).
But this hasn't really helped since the WHMCS files are protected by ioncube so they can't be cached...

Is anyone experiencing similar issues or knows of a way to resolve this?
I've already asked WHMCS support but they weren't of much help :(

They told me the problem would be with my own server since WHMCS is lightweight software...
But I don't see why that would be the case since I have a fast server:

Processor: Intel® Xeon® Processor E3-1230V2 (8M Cache, 3.30 GHz)
Memory: Kingston 32GB (4 x 8GB) DDR3-1333 MHz ECC RAM Unbuffered (KVR1333D3E9S/8G)
SSD: 256GB Crucial M4
Network card: Intel Ethernet Server Adapter I350-T2

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