leeparker - Several things here. If your site is just vanishing and then jumping back, with no movement in between, it's likely that you're seeing results from two different data centers.
When you get the results where you're gone, try adding &filter=0 right after the Google serps page url in your address window... so that the url ends with...
instead of with...
Then click the "Go" button up by your address window. Don't click the "Search" button on Google.
The addition of &filter=0 will show the serps with duplicate pages included. I've been observing that when Google's dupe filters are set high, a page that's been scraped a lot might drop out if Google encounters what appears to be a well-linked dupe. This is one way of detecting that.
If this happens, you'll want to locate the duping pages as well, to confirm that that's what's happening.
In my experience, Google sorts out such dupe issues in two or three or four days. Note that the drop-out is query specific, and happens in particular when Google's link authority "dial" is turned down. At that point, pages ranking by virtue of junk links seem to rise to the surface. This is conjecture, but that's what I think is happening.
It can also happen if your links to a page for a given query are a little bit iffy. It might also happen when Google is re-valuing links, as I think it does periodically, to check algo variants. Again, this is conjecture, but it's based on a fair amount of observation.