Read the thread linked to in the URL for full details Reproducible: Always Steps to Reproduce:
It's due to Hz=1000, it's not trivially as fixable as they make it seem. It's definitely not getting fixed for the 2.4.20 based version. I'll see if I can find a patch for the next version, but I'm not promising anything.
FYI: there are patches for the 2.4 kernels, but they are highly experimental. Use at your own risk. http://www.physik3.uni-rostock.de/tim/kernel/2.4/
Please look at http://www.kernel.org/pub/linux/kernel/people/rml/variable-HZ/v2.4/ and see if that helps. I really don't know how hard it is to make the uptime work correctly, but I think it's fairly important and these patches seem to be all you need. Thanks.
Don't we already have an HZ patch in 'General Setup -> Timer Frequency' in gentoo-sources?