There are many types of DVI adapter, I could type a load of stuff or just point you at Wikipedia.
The key point is that there is no such thing as a DVI adapter. It's just a generic term that covers the overall outline of the cable end, but what you really have is either a DVI-I or DVI-D adapter, in either Single or Dual link capability. Or it may be a DVI-A. Or there are others...!
It's possible that your splitter cable must be of the dual link types, characterised by the longer horizontal bar pin, and your Thunderbolt adapter may or may not be. Shouldn't matter which type, either I (Integrated with analogue signal in the pins above/below the horizontal bar in addition to digital) or D (Digital only) as I imagine you are not subsequently adapting them down to DSUB further down the line, the only thing that matters is if they are both dual link.
So it looks like you need a Thunderbolt/MiniDisplayPort to DVI Dual link - the official apple one is the digital only one without the analogue pins (DVI-D Dual Link), and thus should work, if you are worrying that you do not have the same pinout (i.e. you have DVI-I Dual Link on your splitter, and it looks as though the analogue ones have nothing to connect to) then don't worry, it won't need them.
EDIT - Additional Info
After the comments, I have decided that you have a DMS-59 connector that looks like this:
So what you really need is a MiniDisplay > DMS-59 adapter, and my google-fu suggests that this is not looking like a possibility, I think you would be better served abandoning this cable, and looking for a total replacement, Mini Display Port > 2 x DVI (Single is fine, I or D if you have 2 ports). This may also be a pain to find, and you may end up needing a MDP/Thunderbolt to Dual Link DVI, followed by a Dual Link DVI > 2 X Single Link DVI splitter cable!
Try disabling Automatic Graphics Switching in the System Preferences-Energy Saver. This may be working for me, though I haven't figured out how to reproduce the 1-2 second blanking, so only time will tell.
I'm running 10.8.2 on a new rMBP and have the same issue - The external display goes blank for 1-2 seconds when connected to a 1680 x 1050 display via the HDMI connector and the rMBP is closed and in a stand. There is no movement of the rMBP, the HDMI cable or monitor when this happens.
I have not experienced the same momentary blanking of the rMBP's display when using only the native display.
It doesn't happen often (2-3 times per day) so it's more of an irritation that I don't expect from a nearly $3,000 piece of hardware.
Best Answer
Hooking up multiple adapters in series to get from one type of connector to another, VIA a third type of adapter doesn't always work. However there are enough exceptions to the rule that it is worth trying if you don't mind losing money on unusable adapters or returning said adapters.
There are USB-C to DVI adapters that should work. Amazon sells several makes and models but a simple Google search should turn up a bunch more.