Mountain Lion Freezes 30 Seconds Every Hour

Question

I've recently migrated from a Mac Pro running Lion to a MacBook Pro running Mountain Lion. I migrated using a Time Machine backup and to make a long story short, it was an ordeal, but I've got everything running smoothly now… Everything except for one thing.
Once an hour, everything but the mouse freezes. The clock stops. If time machine is backing up, the backup icon stops moving. Everything stops for about 30 seconds and returns to normal. It happens very consistently on the same minute and the same second every time until a reboot and the one hour clock starts ticking anew from my boot up time.
I thought that maybe Time Machine was the culprit here, but I turned that off and freezes continued happening. Also, there is nothing in my log files that show anything happening at the time of each freeze. This is driving me nuts.
Any help would be appreciated.

Answer 1

How to maintain a Mac
1. Make redundant backups, keeping at least one off site at all times. One backup is not enough. Don’t back up your backups; make them independent of each other. Don’t rely completely on any single backup method, such as Time Machine. If you get an indication that a backup has failed, don't ignore it.
2. Keep your software up to date. In the Software Update preference pane, you can configure automatic notifications of updates to OS X and other Mac App Store products. Some third-party applications from other sources have a similar feature, if you don’t mind letting them phone home. Otherwise you have to check yourself on a regular basis. This is especially important for complex software that modifies the operating system, such as device drivers. Before installing any Apple update, you must check that all such modifications that you use are compatible.
3. Don't install crapware, such as “themes,” "haxies," “add-ons,” “toolbars,” “enhancers," “optimizers,” “accelerators,” “extenders,” “cleaners,” "tune-ups," “defragmenters,” “firewalls,” "barriers," “guardians,” “defenders,” “protectors,” most “plugins,” commercial "virus scanners,” "disk tools," or "utilities." With very few exceptions, this sort of stuff is useless, or worse than useless.
The more actively promoted the product, the more likely it is to be garbage. The most extreme example is the “MacKeeper” scam.
As a rule, the only software you should install is that which directly enables you to do the things you use a computer for — such as creating, communicating, and playing — and does not modify the way other software works. Never install any third-party software unless you know how to uninstall it.
The free anti-malware application ClamXav is not crap, and although it’s not routinely needed, it may be useful in some environments, such as a mixed Mac-Windows enterprise network.
4. Beware of trojans. A trojan is malicious software (“malware”) that the user is duped into installing voluntarily. Such attacks were rare on the Mac platform until sometime in 2011, but are now increasingly common, and increasingly dangerous.
There is some built-in protection against downloading malware, but you can’t rely on it — the attackers are always at least one day ahead of the defense. You can’t rely on third-party protection either. What you can rely on is common-sense awareness — not paranoia, which only makes you more vulnerable.
Never install software from an untrustworthy or unknown source. If in doubt, do some research. Any website that prompts you to install a “codec” or “plugin” that comes from the same site, or an unknown site, is untrustworthy. Software with a corporate brand, such as Adobe Flash Player, must be acquired directly from the developer. No intermediary is acceptable, and don’t trust links unless you know how to parse them. Any file that is automatically downloaded from a web page without your having requested it should go straight into the Trash. A website that claims you have a “virus,” or that anything else is wrong with your computer, is rogue.
In OS X 10.7.5 or later, downloaded applications that have not been digitally signed by a developer registered with Apple are blocked from loading by default. The block can be overridden, but think carefully before you do so.
Because of recurring security issues in Java, it’s best to disable it in your web browsers, if it’s installed. Few websites have Java content nowadays, so you won’t be missing much. This action is mandatory if you’re running any version of OS X older than 10.6.8 with the latest Java update. Note: Java has nothing to do with JavaScript, despite the similar names. Don't install Java unless you're sure you need it. Most users don't.
5. Don't fill up your boot volume. A common mistake is adding more and more large files to your home folder until you start to get warnings that you're out of space, which may be followed in short order by a boot failure. This is more prone to happen on the newer Mac notebooks that come with an internal SSD instead of the traditional hard drive. The drive can be very nearly full before you become aware of the problem. While it's not true that you should or must keep any particular percentage of space free, you should monitor your storage consumption and make sure you're not in immediate danger of using it up. According to Apple documentation, you need at least 9 GB of free space on the startup volume for normal operation.
Use a tool such as the free application OmniDiskSweeper to explore your volume and find out what's taking up the most space. Move rarely-used large files to secondary storage.
6. Relax, don’t do it. Besides the above, no routine maintenance is necessary or beneficial for the vast majority of users; specifically not “cleaning caches,” “zapping the PRAM,” "resetting the SMC," “rebuilding the directory,” “running periodic scripts,” “deleting log files,” “scanning for viruses,” or “repairing permissions.” Such measures are for solving problems as they arise, not for maintenance.
The very height of futility is running an expensive third-party application called “Disk Warrior” when nothing is wrong, or even when something is wrong and you have backups, which you must have. Disk Warrior is a data-salvage tool, not a maintenance tool, and you will never need it if your backups are adequate. Don’t waste money on it or anything like it.