Why is Mandrill not recording click-throughs properly?
There is a known issue with Mandrill click-tracking where sometimes if the URL is too long then Mandrill disables it's click-tracking on that URL. You can see the *Long Links* explanation here: https://mandrill.zendesk.com/hc/en-us/articles/205582897-Why-aren-t-clicks-being-tracked-
For some customers I have seen that no MageMail links are click-tracked at all through Mandrill. MageMail adds some click tracking parameters to each link including things like google analytics UTM codes and several other things - coupon codes, auto login tokens, etc.
I'm currently looking into potential solutions to resolve this, but for the time being you can continue to see click-through data in your Mandrill account and also your Google Analytics account should be able to track click-through sessions as well.
Also, open tracking in Mandrill isn't affected at all by this.