Macbook Pro Thunderbolt and HDMI displays switch on wake up

Hi there,
Currently using a late 2013 15" Macbook Pro., latest version of Mavericks. I have one display hooked up through Thunderbolt->DVI, with a second set up through HDMI->DVI.
There seems to be an issue where on waking the monitors up from sleep mode (about 10 minutes inactivity time) the displays will turn on, immediately go black (inlcuding the Macbook Pro screen), and then switch such that all windows on one are now on the other.
I can't really repliate this, as it seems to just happen randomly. All I can say in my detective work, is that the HDMI->DVI hooked-up monitor tends to take a little more time to turn on after sleep, whereas the Thunderbolt->DVI monitor comes up immediately.
Any help would be greatly appreciated.
Thanks.

I've noticed that the HDMI connection seems to lag the Thunderbolt on wake as well. I haven't had the switching issue, though. I use my Thunderbolt display as the primary (menu bar in the preferences) - maybe try doing that if you're using your HDMI out as the primary.
You can always try resetting the SMC and PRAM as well.

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