Customizing (or fixing) the Flash DVD encoding presets

The Flash DVD export from Encore is actually pretty cool--a great way to build a nice web-deployable video player without having to dink around in Flash (which is something I'm likely to never do). However, the video encoding presets have some issues, and I've not found a way to fix, modify, or add presets.
In particular, when building a Web DVD using widescreen assets, the widescreen encoding presets (both FLV and F4V) encode black lines at the top and bottom of the frame. At first, I thought this was just a problem with the HTML code and that by changing the code, the player would be resized vertically to cover up the black lines (e.g. I thought the black was just the background of the player and the video was "floating" in the player pane). However, when looking at the FLV and F4V files after this didn't work, I realized that the black lines are actually part of the videos. This looks really bad in what would otherwise be a slick presentation.
A little more testing led me to realize that the original assets are not being cropped as they would need to be in order to have the encoded video be properly scaled. I noticed there is no way to modify or add encoding presets from within Encore, so I attempted to edit the EPR (encoding preset) files found in C:\Program Files (x86)\Adobe\Adobe Encore CS5\Presets\Internal (Win 7). The EPR files are basically just XML documents, and one of the first entries is for crop. I tried changing the <CropRect> values to "8,0,8,0" to cut off 8 pixels from the sides, which would allow the video to scale vertically correctly, but this didn't have the desired effect. While it DID crop off 8 pixels on both sides, it didn't scale the video.
Next, I tried opening one of the Web DVD presets in AME and editing it there, thinking it would establish the proper values, and then saving it back to the Internal folder. This didn't work, either; comparing the content of this preset and one of the original ones revealed a few differences--enough to obviously make the tweaked preset not functional.
Now, I've found that I can encode files to the correct cropping and dimensions directly from AME, and drop them in place in the resulting Web DVD folder, and it works fine--but for projects with a lot of assets, this is a pain, especially since I have animated DVD menus (which also need to be separately encoded and replaced) and all of the selection overlays need to be recreated too. This is a huge pain, and while it would be OK for a smaller project, I have about 50 such assets that would have to be recreated. It would be far simpler to just use a custom preset, but I can't figure out how to make that happen.
Hopefully someone can point me in the right direction--this is a great feature of Encore that's rendered unusable because of this silly little oversight. Please help!

Oh, now I see... it seems I had misread the item under:
"About Flash video - Additional applications, servers, and
video service features - Adobe Dreamweaver CS3"
at the following link:
http://www.adobe.com/devnet/flash/articles/video_guide.html
So, I'm back to finding the most practical, affordable,
user-friendly way to do the encoding. Maybe a free or low-cost
third-party program (I swear, someone in TS for Premiere CS3 Pro
told me to search for a free FLV encoder on the web)... and maybe
I'm also back to reconsidering if Flash is even best for my needs
versus QuickTime or WMV format. Now that I think about it, I'm
guessing a lot of those more professional-looking promotional and
educational videos I see a lot on the web these days that use just
a little video box with a very simple player right on the web page
are using QuickTime, not Flash. Does that seem perhaps accurate? Or
are the probably Flash? (Is there a way to look into the properties
or source of such a page and find out?)
Thanks again.
Jay

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