plupload.html5.js is included, in a minified form, inside plupload.full.js. So changing plupload.html5.js will do you no good.
I'd think the quickest way to fix your problem is to stop pulling in plupload.full.js and instead include only the required scripts for your application. Here is a very simple example that uses the core plupload and the htm4 runtime:
https://gist.github.com/815706
Since you are not using the jquery widgits, if you pull in the same .js files shown in the example, plus add the .js files for the other runtimes you are using everything should work. You can then change the plupload.html5.js to fix the bug.