Best way to export flash movie for JAVA

Here is my dilema. I get all kinds of flash movies to post to our site. I had been asking for a final output of  .swf, whenever possible. Occassionally I get some videos that have a player and I wind up with .swf and some related FLV files, which we always have problems with in our JAVA environment. We have issues locating the player files, sometimes they don't play for people with particular browsers etc.. The coders tell me that it is a problem with the "base" locations, and recommend that we get a single swf file and have the videos and players embedded into the .swf. They tell me that the browser sometimes cannot find  the supporting files, and that it forces them to post the flash files on the root directory. Any ideas what might be happening here?
One other thing - I currently have an embedded swf file on one of our sites. It seems pretty heavy and skips - our Flash Developer did not include a loader. I sent it back to him to compress the file and include the swf. The developer is telling me that compressing the file won't do anything for me an that we should export it as an FLV file or have the FLV load into the swf. For one thing this is not a video - so I am not understanding why we would need an FLV. Am I misunderstanding something here.
Thanks!

Thanks again Winston. (You helped me out in the past).
In my playing around, I was leaning toward AIC with a compressor pre-set of 1080i or p would give me decent results on export. I'm still a little confused over a number of the other options, and this seemed simplistic. (I'm still learning here as I go).
One question on that though if you would. Am I best off leaving the FPS settings to current? I am assuming I can experiment with that if I want to keep a computer copy, but for back to tape purposes, that seems to make sense to my simple mind.
On a side note, I was quite surprised at how good the default "large" export looks when viewed on the computer. I may keep that as my default for iTunes\Front Row.
Thanks again.

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