Thanks for answering all the questions Richie ;)
I think got the problem now, it happening because of the float left. I will most likely fix that soon. Also you can fix is yourself right now, see below.
Short answer: Add a maxwidth to shortcodes that you want to align to a side (makes no sense if they have 100% width anyway) [youtube id="TYB8agv1Dwk" mode="normal" align="left" maxwidth="400"]
Long answer:
1. Ideally you should never install Colorbox, never use thumbnail mode since you not wanted it in the first place. Even if I said so. Trying something you not want started the confusion. I guessed you wanted it.
5. What I meant was not not shortcode attributes. I meant the real options. This plug has a options page. In the older versions before 3.0 it was under 'Plugins' on the Admin Dashboard not its under 'Settings'.
I advice you to not to use the mode attribute in your Shortcodes if you do not want to use the thumbnail mode anyway, just set mode -> normal in options (it should be by default). Then all your shortcode will be use normal mode. If you one day decide you want all videos to be thumbnails, you can just change that options and all videos with no mode= set will change. I recently wrote a short documentation on my site that might explain it better.
It looks like you not use the float option on this page http://beara.biz/beara-video/ so this was the page that did not broke after the update I guess?
You can also fix the floats = invisible issue right now without any update with simply setting the 'maxwidth' either inside options or inside as url/shortcode paramater.
You know the align attribute makes not much sense with the normal mode without a maximal width anyway since if they are have 100% width they cant really align/float anywhere. Try it out, it should work.
I also had this idea now of outputting some invisible data on peoples pages about what attributes and options they use so I not need to guess/ask every time.
In the end your issue and reporting now finally helped me and provoked that idea, thanks ;)