I have seen few issues with BMW Alpine kits.
Worst: problem with few amplifiers of alpine kit. If your sub was cooked twice, then amp should be replaced before headunit.
Also consider what mob17 has mentioned. What settings are you bass and treble and what sort of volume are you on most of the time?
Here is trouble shoot guide for you guys who are having issues.
1- Check that your kit is installed by colour macthing the wires and not by manual of alpine kit (for LCI alpine kit).
2- If that is correct, please check your harness thoroughly. There may be a wire which is getting earth or due to pressure, it is exposed and getting earthed. (Raf555, especially you mate).
3- If you have installed by BMW, were you car coded to hi-fi (if applicable)?
4- Check the impedence of your drivers by voltmeter and make sure readings are same. If there is a difference, get a pair replaced under warranty. If you run out of warrnty, shop for used pair.
5- If your kit is still frying your drivers, then contact your kit provider and your amp should be changed if under warranty. If out of warranty, then no other options of living with it.
6- If all other measures are failed to resolve your issue, then exhange your head unit with yours mate and see if that helps.
If you follow these, you should be able to resolve the issues.