Like I said...Quit a nice challenge you've got here :)
Although it's not exactly the way Ninja Shadowbox is expected to work.
Good job on the skin, though. Just keep using the zips because that will be the most effective way since you are using the latest JWPlayer.
The problem is the way you combine Ninja Shadowbox with calling directly the FLV player and it's parameters.
Other needed internal scripts, parameters, commands are by-passed this way.
Now, some of the parameters for the FLV player which are called directly within the syntax, will do their job but some are hardcoded in the internal scripts from Ninja Shadowbox. I tried to find a way to modify it for you but that could be conflicting when you use Ninja Shadowbox for other purposes.
But since I love Ninja Shadowbox and it's way you can play around with stuff, I like it to approach things in another way. There are more ways that lead to Rome, you know.
One important thing is that the JWPlayer makes use of FlashVars.
These are simply parameters needed to pass to the FLV player to make it fully functional.
Some of these FlashVars are hardcoded, and some are not, within Ninja Shadowbox.
FlashVars are components of the Adobe Flash Player, which you have to install locally in order to be able to watch Flash based movies (FLV, SWF, etc).
So, this is something that can't be controlled by Ninja Shadowbox nor by the JWPlayer. They only make use of it by passing the needed parameters.
Normally, if you use the JWPlayer as a standalone player you can pass parameters all you like.
But that will only work properly if you make use of the <object> and <embed> HTML tags.
But, using it with shadowbox is yet to discover how.
Since I'm a fan of Ninja Shadowbox and multimedia used in websites, I've experimented a lot with it.
I think I'm able to make it work the way you want.
In fact you use the standalone version of the JWPlayer (for use with subtitles) since you call it directly in your syntax.
This way Ninja Shadowbox listens only to the rel attribute command to popup the shadowbox window and passes only customized parameters (set in the Module and Advanced Parameters). But still loads all the scripts needed for Ninja Shadowbox. This might give a conflict between things.
Also, the scripts from Ninja Shadowbox are a bit outdated (due to license policies), so the general coding is based on the scripts used/integrated at that time. I have no other explanation, but I think it's fairly close.
That said, we still don't have a proper workaround.
So I'm going to give you this work around to make it work.
1) Paste this in the article where the FLV link is, use the html editor to do so:
2) Replace your current syntax with this one (allowfullscreen is gone, not needed anymore):
<a href="http://www.elevenfox.de/player.swf?autostart=true&skin=http://www.elevenfox.de/beelden.zip&plugins=captions&captions.file=http://www.elevenfox.de/media/polysics-each-life-each-end-budokan.srt&file=http://www.elevenfox.de/media/polysics-each-life-each-end-budokan.flv" title="POLYSICS - Each Life Each End - LIVE at Budokan" rel="shadowbox;width=624;height=360;">KAYO カヨ 2</a>
3) unzip the attached modified shadowbox-swf.js and upload it to /modules/mod_ninja_shadowbox/ninja_shadowbox/js/player/ (backup original first).
This should do the trick ;)
Note that this a work around based on this topic.
Might not work for other users.
Let me know how it goes.
Have a nice a nice day ;)