Apple Applications cannot Access the Internet, Others can

I've owned my MacBook for about 1.5 years now and it's starting to have some stability issues. Daily hard-locks are becoming the norm. I suspect hard drive issues may be to blame. I have repaired permissions and verified and repaired the disk. That seemed to help for a little while, but this latest problem is throwing me for a loop...
Apple applications cannot access the Internet. Apple Mail (RSS, POP, ad IMAP), Safari, iTunes (PodCasts, iTunes Store), and Software Update all time out while trying to contact servers. Firefox, OpenVPN, command line SSH, ping, etc, all have no problems.
My next step is a reformat, but this week is a really inconvenient time for me to do a backup and restore and I'd love a quick-fix if there is one. Any suggestions?

Thanks. I just realized that is was serious user error. I forgot I had enabled Socks proxy in Internet connections a couple of days ago and that my Mac apps would still be using that while my other apps would not. Thanks!

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