I've encoutred problems with this issue, in the documenation the box hides but i encoutred problems with it.
I've fixed this using display property instead of the left property.
Since i'm only using the regular select box, I've changed (uncompressed version):
line 370 changed "left: -9999px;" to "display:none;"
line 633 : display:block;
(as i remember)
Hope this helps anyone and i think in general the next version should be like this.
Chosen uses positioning instead of display because of significant performance issues when hundreds of options are involved. Using left positioning avoids scroll issues and solves the performance problem.