The installation of Mibew Messenger on a site means that one is running installer, then generating a button as a javascript code, and then inserting the given code into the markup of the site. That's all.
If you can log into Mibew Messenger administrative interface and generate the javascript code, the installation is fine.
And there should be no interaction between Mibew Messenger and any other software (be it Drupal, or Joomla, or Wordpress, or anything else).
As far as I can understand, you're trying to somehow make use of the internal libraries of Mibew Messenger. They are not supposed to be used that way. BTW, one of the basic reasons for the creation of Mibew Messenger 2 was an aspiration to make it possible to create agile third-party solutions based upon Mibew.
To sum it up.
1. Stop calling your actions an installation. You're confusing everyone including yourself. The process you're into should be called integration.
2. I really doubt that someone will try to recreate the errors and to find a solution for your troubles caused by mixing the code of almost outdated Mibew Messenger 1.6.x and Drupal (BTW, Drupal 6 that you've mentioned is almost outdated too). Good luck with that.
3. You'd better take a look at Mibew Messenger 2.0 and try to somehow make use of its new abilities. Though even in that case you'd better ask a concrete questions. Sometimes one explores the troubles and writes a code for other people just for fun, but there are not too much third party developers of that kind in the Mibew Messenger community...