Avid/Firestore workflow, NEED HELP!!!!!

Matt E.- Having some real issues with workflow. I have downloaded and installed the new firmwear update. I can see all of my recorded clips on the HVX200 when played back from the Firestore, but when I copy the MXF files to (Avid MediaFilesMXF1 folder on any given partition) not all of the files show up in the media tool. (For example shot 45 clips, only 29 of them show up in Media Tool.)
I have "organized P2" after shooting to the FS100. and copied (not dragged) the video and audio file folders to an Avid drive partition. I have had discussions with Avid Tech support, but they have just received their first unit for testing on their end. I am trying to stay away from P2 cards and just work with FS100s. I spent 4K and bought two of the FS100s. Been fighting with this for over three weeks, starting to lose work, with not being able to promise DTE. BTW- I have tried this workflow on a PC HP XW8000 Adrenaline ver 2.24, 3 gigs ram, 1.7 terrbytes Avid drives AND Compaq nw8000 laptop with Avid Xpress HD ver. 5.2.4. Footage was shot 16:9 30P Pro50.

My background:

Director/DP - 20 years
Avid owner - since 1995
Firestore owner - 3 weeks
Frustration level - high to boiling point

Any insight would be greatly appreciated.