Dear baldaszti,
Maybe I missed something in the discussion (forgive me...) o I am asking something obvious, but why you have to reconfigure the whole router so soon? I really can't understand.

It's not so soon. The time is irrelevant, the point is, if we need to upload the configuration from the central management sever, we can do it once, and never again. The reset is necessary because the /export command generates such clis that it gives error on /import (it's about using "set" and "add"). It can be loaded only if the device has empty config (that's fine, many company use this method). And we cannot use any tool that compares and generate clis, it's a question of responsibility (we have to send the commands unchanged to the device, so if an error occurs, it's the administrator's fault, not some program bug).

I've used Milliscript for processing export files and never had a problem. Have you seen the latest version - http://wiki.mikrotik.com/wiki/Milliscript ?

It's a godsend!

Rgds,
Mark.

if you are that concerned about security you should know that keeping those keys is insecure when router is completely reconfigured.

Dear Mikrotik,

Two months passed, the 5.7 is out, and host key still regenerating.
You did not manage to put a simple "if()" in your code within 2 months. This means your RouterOS is the only software in our arsenal that cannot save it's configuration in cli format and load it back again, so management decided to throw all of them out. Congratulations! I'm pretty sure you'll have no further orders from my government (the owner of our company).

Don't tell me you didn't had the chance. Sic transit gloria mundi!