Did solve part of your problems!
Changed your preloader a bit!
But the most important change you have to make is to add a stop(); action at the end of your Scene 1, otherwise the movie loops back to the beginning, which is the preloader.
Of course putting a stop(); action - (add an actions layer, select the last frame, insert a keyframe (F6), and add the stop(); action) - stops your lines from moving. That's why you have to convert them into a movie clip, in the same manner you have done it with your logos' movie clip. I have done so, purposely re-positioning the movie clip, so that's why you see a second set of moving lines, while your's have stopped.
In fact, once this is done, this can be but a 1 frame scene with a stop action on it.
As for smoothing out the transition between the preloader and the main movie, you could fade in your navigation bar (motion tween with alpha) and/or your movie clips (lines and logos), that would definately smooth it out!
Please note that some of your links will not show up from my site, since I don't have all the htmls you're calling.
Having some troubles with all of my free hosts, so if you want me to send you the corrected .fla, send me your address at oldnewbie@hotmail.com
Regards,
ldnewbie