What steps will reproduce the problem?
(1) Start Chrome with --site-per-process
(2) Open a tab so you have two tabs.  Type http://csreis.github.io/tests/cross-site-iframe-simple.html into the omnibox in the first tab.
(3) Right after pressing enter, switch to the second tab.
(4) Wait a bit for the first tab to finish loading.
(6) Switch back to the first tab.

At this point, the OOPIF is not visible.  The subframe process does show up in process manager, and clicking on the second tab and then back to the first tab again makes the OOPIF show up.  So this seems to be some sort of visibility issue.  Note that document.visibilityState shows "visible" for the OOPIF when it's not showing.

I reproed this on 54.0.2795.0 Mac Canary and 53.0.2785.8 Linux dev.  

Even simpler repro: insert <a href="http://csreis.github.io/tests/cross-site-iframe-simple.html">link</a> and ctrl-click it.  After waiting for the tab to load, switch to it.

It seems that basically any OOPIF that finishes loading while in an inactive tab won't initially show up.  

This affects --isolate-extensions as well.  I've tried right-clicking the "Beautify FB" extension's Options link and "Open link in new tab".  After waiting for the new tab to load and switching to it, the Facebook subframe doesn't show up.  This seems pretty bad, so I'm adding the blocking label.