Removing closed caption line 21

This might not be a topic for this forum, but I thought it was worth a try.
I work at a TV station where we recently relaunched our master control that is now 100% digitally managed. All of our programming, commercials, etc is Quicktime run by software called BugTV. Here's the problem.
We run programming with closed captioning and then using BugTV software and a Kona card, we add a station ID bug (Quicktime Animation codec RGBA) ontop of the programming.
What is happening is the two Quicktimes running simultaneously takes out the closed captioning. There is a collision of the two sources of line 21 that removes the captioning all together. Without the staion ID running the captioning comes through just fine. AJA tech support suggests we wipe out the line 21 on the bug (RGBA) file and it should allow for the underlying programming closed captioning to pass through.
My question, is there someway to remove line 21 from a file or scrub it clean so it doesnt interfere with other sources? Does anybody have experience doing this?

I managed to solve the problem with the help of the people at Bug TV. If I render the motion logo .mov at 720x486 as opposed to 720x480 it allows the closed captioning from the programming to pass through without a problem. I'm not sure how or why but it works.
Thanks for your help and interest Tim. I do have to correct you about our mater control set up. We are operating a fully-functional master control via Bug TV software without any hardware apart from a PowerMac G5, Kona card for running downstream keys and a 48 Terabyte video server.
All of our programming is ingested from tape, managed and played back on-air using Bug TV software. Like I said before, it's quite incredible and is, in my opinion, the way TV stations will be run in the near future.
Tape? What's a tape?

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