Automated configuration tools (such as CFEngine, Puppet, or Chef) allow you to avoid SnowflakeServers by providing recipes to describe the configuration of elements of a server. Configuration synchronization continually applies these specifications, either on a regular schedule or when it changes, to server instances throughout their lifetime. If someone makes a change to a server outside the tool, it will be reverted to the centrally specified configuration the next time the server is synchronized. If some configuration change is needed, it's made in the configuration specification (recipes, manifests, or whatever the particular configuration tool calls it), and is then applied to all relevant servers across the infrastructure.
In theory, once a server has been created, configuration synchronization will keep it up to date, applying upgrades and patches and preventing configuration drift for a potentially long lifetime.
In practice, however, it isn't feasible to keep servers completely consistent using current automated configuration management tools, so over time configuration synchronization leads to inconsistency. 
Each element of server configuration managed by an automated tool requires work to write, test, and maintain the recipe or manifest. It simply isn't reasonable to attempt to manage every single element of a typical server using these tools. There are far too many of them. And for each additional element you do specify, the work involved grows non-linearly thanks to the potential interactions, integrations, and dependencies between them.
Software packages are a particular challenge, given the dependencies they may have on yet more packages. Tools such as yum, apt-get, gems, etc. automatically work out dependencies and install them from repositories. So a large number of the packages on a system are only implicitly managed, and may change without notice. Although you can micro-manage the versions and dependencies of software packages installed, it's an intractable job considering the number of packages involved.
If managing the stuff you want to have on your server is difficult, managing the things you don't want is worse, given there are an effectively inifinite number of them. Current configuration management tools require you to explicitly list each file, package, or other element you want removed if found. This means additional things can be manually added onto some servers, creating inconsistent and unexpected behaviour.
In reality, people using automated configuration tools get by well enough without specifying 100% of the configurable surface area of their servers. Teams apply the 80/20 rule to automated configuration, focusing 80% (or more like 95%) of their attention on defining that 20% (or 5%) of the system which is most relevant to their particular needs, leaving the rest to the defaults installed by the base OS. So the majority of the system is not under automated configuration, and generally, this works. Unfortuantely, when it doesn't - when some part of the system not managed by automation tools does cause an issue, the effects are unexpected and can be difficult to track down.
This problem grows worse over the lifespan of a server, and with the frequency of change. The longer a server stays up, the more it may deviate from other servers, especially newer ones.
This issue leads some people to use PhoenixServers. By ensuring that a server's lifespan is kept short, frequently rebuilding fresh ones from a base image, the potential for configuration drift is kept small, without the overhead of specifying more of the server's configuration in a management tool than is really necessary. Taking the phoenix server to its logical conclusion leads to ImmutableServers, which avoid any changes made to a server during it's lifespan.
1: Vendor Aspirations
My colleague Max Lincoln provided these references to configuration tool vendors' aspirations around total system configuration:
- "Create a blueprint of your infrastructure - so it can be built or rebuilt consistently from scratch in minutes" - Opscode Chef
- "Eliminate configuration drift and reduce outages" - Puppetlabs
- "CFEngine then continuously corrects configuration drift, keeping systems in compliance with their Desired State." - CFEngine