I believe the .FDR file basically is a data dump when you remove the text header from the beginning of it. The 64 kilobyte pages are laid out as in figure 4.2-2 of the PDF document on my web page that I referred to in my reply to Myriad. There are two flight data streams in the .FDR file as in the same figure.
It could be -- I have no way to tell. However, if the .FDR is a copy of the flash image, it should also have some other interesting properties, like old flights that are gradually being overwritten. At the end of the record should be a chunk of cleared memory corresponding to the last block erase, followed by remnants of the overwritten data. There may also be EDAC bits in play, i.e. every 16-bit word is actually represented by 20 bits, that kind of thing.
I'm stabbing in the dark, however; I've never worked on an FDR directly and I don't know how it was configured. We would need a system expert and this information is probably proprietary.
When you refer to the file extracted by the NTSB do you mean the .CSV file?
The .FDR file comes from NTSB as well, I think. It also must have some kind of filtering applied, though whether it's heavy filtering or very light I just don't know. It may be close enough to the original image that your analysis is valid.
The NTSB report says that "The remaining parameters either were not recorded properly or were not confirmed to have been recorded properly". I do not interpret this as definitely saying that some parameters were found to not be recorded properly, it could be that the NTSB did not try to confirm that any of the parameters that they did not validate were recorded properly.
That's my reading as well. I think the NTSB simply had some out-of-date packet definitions, or there was some mild configuration management problem at American Airlines that could be rectified without too much effort. I believe with more effort the invalidated parameters could be reconstructed. NTSB may not have bothered -- as I mentioned somewhere in this monster thread, the usual purpose of FDR analysis is to understand why the accident happened, and since the cause in this case is straightforward, they may have done only a cursory data inspection. On other flights, notably AA 587, they worked much harder to extract fragmentary data than they did here, and for good reason.
Incidentally, have you looked at the UA 93 FDR? We see a similar phenomenon there, where the last couple of frames have time markers but no valid data. Here, however, the amount of missing data is thought to be only a second or so, rather than ~6 seconds as we see here, but I think the phenomenology is similar.