Some questions

Strange, I thought I had answered it few days ago.
Anyway, here it is again:

1. I can't do much for you on that end. Reduce the comparison to only 2 then, or remove the module of the right.

2. I tried IE, chrome and Firefox and it works on all three...

3. That's because of your browser which keeps the check boxes selection when going back in the history.
On IE, the checkbox status is not kept, on FF the page displays exactly the same as when you left it. It only is a problem in chrome where the checkboxes get selected while the button isn't displayed.

4. Strange indeed. Looking at the JS it sounds like the limit is at 5 ont he listing of products.
Simple fix:
go in the menu Display->Views, edit the file 'listing' of the view product and change the line:
if(compare_list.length < <?php echo $this->params->get('compare_limit',5); ?> ) {

to:
if(compare_list.length < 3 ) {