As you know, the .PEK files are the Waveform Display. The .CFA files are the Conformed Audio. These are necessary for PrPro to edit, and to have the Waveform displayed.
My guess would be that PrPro is loosing these, because of the networked environment. I'd try with the Assets copied to the local HDD, and make sure that all Scratch Disks are located locally, as well. If this works, once PrPro has gone through the process of .PEK and .CFA writing, so long as these files are not moved, that should be it, and PrPro should be able to find these files and use them, without additional Conforming and PEK generation.
I've had similar occur on mapped network drives, and just doing the copy and redirecting PrPro to those copies (Relink Media) has cured it. I now only use network drives as storage for Assets, and not to provide same to PrPro for editing.
Thank you for the advice. I have noticed whenever I create a project that is located in a floder on the desktop, or more specifically the local hard drive I do not have these problems. My boss knows more about Macs than I do, so I will show him your post.
This is in anticipation of an internal HDD real estate problem:
As I shuttle Projects between my laptop and my workstation, I often have Projects on externals. Though it is not the most efficient thing to do, I locate my Scratch Disks within the Project structure on the externals. I also have copied all Assets to appropriate folders in this structure, so the entire Project is portable. I use FW-800's (eSATA would be even better), and can edit easily and efficiently to/from those externals. Though I have multiple farily large and fast SATA II internals on both machines, I would then loose the portability, so I live with the slowdown of the FW-800 vs SATA II connection for those Projects.