F4V File Loses 30 Minutes of 1 Hour Presentation

Question

My client used a conferencing company to host their meeting. They wanted to provide me with a complete finished file (with audio added) for upload to the website. They use Quicktime exclusively for their client projects. The presentation was strictly a Powerpoint and no video. The conferencing company asked how I wanted the file. I asked for a file I could use in a flash movie. The provided me with a f4v that they had married the ppt and the audio files together.
I tested thier *sample* f4v file they sent me prior to the meeting (containing a movie of an interview) by putting it in AME and encoding it for a smaller flv in several bracketed settings. These all loaded into Dreamweaver fine and played out ok on my test pages.
When I received the fv4 of the presentation file, I noted it was 206mb. I began trying to encode it to reduce the size as much as possible so it could load ok on the web. For two days I struggled with settings and each result (either f4v or flv)  produced unacceptable results (Powerpoint slides blurry) when I pulled it into Flash Professional. I finally used what I thought was the lowest quality setting I could get away with and a much smaller dimension. This movie was a bit better but stil not up to my standards.
However something continued to seem to be wrong about all the .swf files I was creating. They seemed to have the original 56 slides, but the audio seemed to not track with the slides properly. It was 3 days after I received the file that it dawned on me that the file must be corrupted at 27 min. All other video handlers (including MS file managment)  that I had on my machine showed the same thing, a file 27 min. long. I thought that was the length of the meeting! All the slides were there, but the audio was abbreviated to from 59 to 27 min and the file length was 27 min.
On a hunch, since this company uses Quicktime, I pulled up my "never used" Quicktime player. I don't even like having this on my machine because it is insidious. I played the f4v file in it and wouldn't you know, the file was actually 59 min long! And this included all the audio. But I needed to have the whole file to encode it in AME. Since nothing else I had used, including Flash Media Playback, could see the other 30 minutes of the file I was forced to purchase the professional version of Quicktime to export the file and get it into Flash. Drat.
I eventually gave up on the .swf movie for the web and took the ppt file, added the audio files (that I extracted using Quicktime), edited them in Soundbooth and then used a third party packager to make a flash movie. Worked like a charm.
However, the client now wants to know why I "don't know what I am doing." I need to know, since I am no expert on the art of encoding, is it possible that this file was corrupted by Quicktime when it was encoded by them? And why would it behave as a corrupted file to all my Adobe products, but not to Quicktime?
Why would every video handler I have (that can handle a f4v) see and play this file at exactly the same (wrong) length? It never worked in the online Flash Media Playback either, giving me a vague message about a problem at this time. So what does Adobe Media Encoder see that causes it, when encoding, to take the 56 slides and compress them into half the time of the original presentation and chop off the last half hour of audio? Should I have known this would happen?
I know this is Monday morning quarterbacking, but I am really curious. And it would help to have my ducks in a row when talking with the client.
Thanks

Answer 1

Sorry for the delay in getting back.  I had woken around 3:30AM and got up to check the status of the 2nd export attempt, and when I found the same situation as the first attempt, stayed up to post here and see what reponses hopefully might be here when I got up in the morning.
Ann, there are no gaps on the time line as it is one continuous file, due I guess in how I saved it to the other disc.  Just uploaded the one really good Neat profile I got on the individual file segments in the browser from the RAID drive that I had placed on the time line with the first sequence.  The first three of those left a bit more noise in some spots, but a lot of noise still crawling on the right cheek of the CEO in the low light he saddled us with.  Luckily the 4 try Neat really nailed it. 
BUT....after typing the above I just re-inserted the Lexar flash drive and brought up its info and yep it does say, "MS-DOS (FAT 32)"    Uggghhhh!  Bought it a week and a half ago from Office Depot in town.  Wasn't cheap.... $178 plus tax.  Still have my receipt, hopefully they will refund.  This type of scenario is exactly why I bought that large a size ....64gb.  To be able to have enough space to leave shooting job with a client if necessary and they could mail it back to me when the job was offloaded.
Is there any kind of flash drive that size then, that doesn't have the file size restriction I can pick up from on line or like a Frys please?  I think the incredibly slow export was due to the 2.0 USB and all the Neat noise reducing information, plus HD codec I guess.  7 1/2 hour export and only 18 minutes out of the hour covered..  Are there any other convenient options to leave with a client, with maybe SATA connection, which would be safe to ship back to me in these situations that could take the jostling from shipping?
Thanks very much
Ron