Video uploads and converts to flv, but: will not play, database is not updated, and cron breaks

First, before I describe my issue a popular initial response will be "what do you have in your php.ini and/or htaccess file?"

So here are my settings:
post_max_size=200M
upload_max_filesize=100M
max_execution_time=1000
max_input_time=1000

*I am using a custom php.ini because Site5 (my host) runs Apache as a CGI so I cannot use htaccess

Here is the problem I am running into with Flashvideo module:
-I can upload a video (wmv) using a node type
-FFMPEG converts it to flv no problem on the next cron run
-The thumbnail (jpg) is also created
-However, after conversion the follow-up database entries (for example, setting "status" of flv to 3) are not made (the status is left at 1)
--Note: If I manually go in and change status to 3, the video still will not play and I get the "video is not currently available" png image
-Also, after conversion *cron hangs* for a couple of hours
--By cron hanging, I mean that cron doesn't fire after five minutes as it is supposed to and when I try to run cron manually in Drupal status report I get the "cron run failed" message
--Checking my logs last night, it looks like it took cron right around two hours to resume running again

This happens every time I upload a video for conversion, and is repeatable. (I can get cron running again by going after the cron_semaphore variable via this handy blog post http://www.digitaledgesw.com/node/21#comment-38)

*Now, to make things more interesting:*
-After cron is reset
-If I delete the attached video in the node *but not the node itself*
-Then reupload the wmv file to the original node I just deleted the *same* wmv file from...
--The database entries are then made
--**the video will play in Player.swf***
--And cron does not break

Other notes:
-When I delete a Video node, the .wmv and .jpg files delete from the server, but not the .flv file
-Flashvideo is using the main Drupal /files directory for video uploading and output (in other words, the wmv, the jog, the flv and Player.swf are all in /files)

I hope this is enough information to help with discussion, etc.

Best,
Shane