Yeah, JS minification can be really tricky, but sometimes worthwhile for script-heavy sites hosted on slow servers. In this case, we did minify most of our JS, which shaved about 3 seconds off of average page load times when using W3TC. Our only issue on this site was with inline JS minification, and that too only with Shareaholic.
But we don't particularly need inline JS minification on this site because we didn't use much inline JS (just a few short scripts that are annoyingly inserted inline by plugins instead of using external scripts).
So. this post was meant as a headsup for those who might be affected, hopefully to save them some troubleshooting time. (But of course if the devs of either Shareaholic or W3TC can find a fix, all the better for those who wish to use inline JS minification.)
Actually, in the end, after configuring W3TC to its optimum settings and testing page load times, we then deactivated W3TC and set up WP Super Cache to do a comparison, since every site and host context is different and you never know. The result: WP Super Cache resulted in page loads that were 2-3 times as fast as with the best W3TC settings. So, while one sometimes gets better results with W3TC, for this site we wound up going with WP Super Cache. Moral of the story: It's worth testing both if performance matters.