Hello everyone.... For what it is worth I have been struggling for the last 2 days with similar issues and finally came up with a solution using variables that I learned from here!
At first all I could upload was .flv files and everthing processed and was in the proper folders but the .flv had a O size value. That was corrected by commenting out the second conversion configuration in the /include/settings/video_conversion.php file and using the first option. That brought me to the file size problem discussed here. These are the settings that corrected my issue.

First I added the following at the bottom of my .htaccess file as suggested.....

php_value max_input_time 600
php_value max_execution_time 600
php_value post_max_size 200M

Then set site settings in Admin to......

Video Processing: Background Processing
Create Thumbnail: ffmpeg
Flvtool: Disabled

The key in my case was the background processing. Before I changed to that process it would time out and give the Explorer "Page not Found". When I went to the admin the file was there but was stuck with the "conversion started" statement which never completed. I could manually activate the file but it did not have total time in the "duration" field. The conversion process was only half complete and the option to reconvert was not available. Hope this helps sombody!

Good luck All