Current version of Chrome 47.0.2526.106 resolves this behavior.
I've been experiencing some short machine freezes while using both OS X Yosemite and El Capitan. Could not figure this out for a while and I think I found the culprit.
These short freezes last about 2-4 seconds, only appear while Chrome (production) is running, and appear to freeze not just Chrome but the entire machine.
When Chrome runs a software update in the background, it throws the following message in the console
"triggered DYLD shared region unnest for map".
The Chromium team knows about this issue. As mentioned in the issue thread, it appears that a bunch of messages get jammed into the system log, but it may not actually be the messages that are the issue.
Hopefully a proper fix is released for this soon, I've been struggling to find this issue for a while.