I've also had issues with Steam overlays. Even when enabled, sometimes the purchase just won't go through. The very simple alternative is just to log into the website and make the purchase there. If you've added things to your basket in-game, it will even "remember", so you literally just log in, complete the purchase, return to the game, and you're good to go.
For anyone having issues I really recommend posting about it on S3's forums as opposed to here, because other than the above advice there really isn't anything else we can do.