WHMCS update broken site and nonstandard WHMCS installation directory

We recently performed the update for your WHMCS plugin and it broke our multi-site. Many of the domain mapped sites would no longer load. I’ve read some other problems with the update here on your boards but I haven’t seen anyone refer specifically to the issue of the WHMCS installation being in a nonstandard directory. In other words, our whmcs install is in a directory called billing rather than the default directory named whmcs. When we deactivate the plugin, our sites load properly. Would a nonstandard directory name cause the plugin to break our site?? If so how do I fix? If not, can you suggest an explanation? When can we expect an update to the update?