When locale.inc's _locale_parse_js_file() function tries to parse a javascript filepath with a querystring appended to it, it considers the entire string to be a path. Here's my (very simple) patch:
From locale.inc
function _locale_parse_js_file($filepath) {
global $language;
// Load the JavaScript file.
// BEGIN PATCH
$s = strpos($filepath,'?');
if ( $s ) $filepath = substr($filepath,0,$s);
// END PATCH
$file = file_get_contents($filepath);
…
(snip)
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