We just set up Callwhere Call accounting for a client that has a Merlin legend r7.0. inbound and outbound calls are seeming to collect correctly, except that SOME outbound calls from one extension (x106) will not show the outbound number dialed. Most of there calls do show it, but one out of 5 or so wont. It is not based on duration or line number used.

Have you removed the call accounting piece from the equation? I'd hook up my laptop directly to the SMDR port and run hyperterminal or procomm or some other terminal software. Make a bunch of test calls and see if they all report in the raw SMDR stream.
Mike