To those using WHMCS:

Anybody have tickets created and it's missing in the SUPPORT TICKETS MAIL IMPORT LOG? If this happens, it usually means the customer did not get a confirmation email for the ticket creation nor will he/she receive any of the replies you've sent.

Are you experiencing this problem? If so, how did you fix it?

Note: this doesn't happen for every ticket. Only a selected few. Weird thing is when I test it, everything is working the way it should be but it does happen.

Have you tried contacting the support team at WHMCS.com ? I could remember a few occasions when I use to use WHMCS of the exact same problem.

I was told if the ticket is submitted directly from the clientarea, it does not get logged.

It would make sense that Dan is right here.
If you're logging the tickets via the helpdesk (ie: through a browser), why send a confirmation mail, or log it as a 'email', right?