I was having this issue just yesterday and did a bit of de-bugging. Here's what I found:
I had already made some alterations to the wordpress-popular-posts.php file, namely inserting at the top of the file before the first line:
I haven't run it in this mode with all of the minification features intact but I think it might work. I did get rid of the comment and line break settings in W3 as success2be suggested. Running it in that mode after clearing the cache did nothing for me.
I also did a few other minor tweaks, so I can't say definitively that I have isolated the problem.
Two things did work though:
2. Running JS minify without the jquery file minified (/wp-includes/js/jquery/jquery.js.gzip)
What I imagine is happening is that WPP depends on jquery in some way and that minifying it breaks the counter function. I suspect you can minify everything exactly as you want and leave out jquery and all would be well (I'm no coder so take this with a pinch of salt).
That's my two cents: jquery is causing the conflict.