That's absolutely astonishing. I'm still unable to reproduce the issue, and thus have no ideas about any possible solution...  

Correct me if I'm wrong. To reproduce the issue one should:
1. Setup standard LAMP system (let it be Debian 8 with Apache 2.4.10, PHP 5.6.30, and multiple modules and PHP extensions as was described 
here).
2. Download our official distribution: 
https://mibew.org/download23. Unpack the distribution at 
/<server document root>/mibew/4. Prepare valid configuration for Mibew Messenger (i.e. 
configs/config.yml)
5. Visit 
http://<server>/mibew/installRight? Is it a 
full list of steps to reproduce the issue 
without any missed parts?