I was trying to hold off on bumping this because I don't want to be spammy, but here is what I have found so far.
Making a sprite collection with platform support for 1x and 2x loadable means that it has 3 entries in the tk2dSystem, 1 for the collection, 1 for the 1x, and 1 for the 2x. Rebuilding the index removes the entry for the collection but keeps the entries for the 1x and 2x.
We are using svn, so this means that the tk2d Resource folder is ignored, and everyone rebuilds the index after updating causing the entry for the collection to be removed. It is possible to get this back by opening the collection editor and checking the loadable box on and off again (This does not require the collection to be committed). When this is present the data that gets loaded is not the platform data, and the sprite that shows up is for the correct platform.
If I rebuild the tk2d Index then the data that is loaded is always the 1x collection data. Normally this can be solved with the fix that I mentioned above, by toggling the collection loadable check box. However if unity is restarted after the index is rebuild (before the resource entry has been recreated) then it will continue to load the 1x graphics. Even if I toggle the loadable check box I need to commit the collection for it to load the platforms correctly, which is time consuming when we have around 45 collections to worry about.
This is with out any modifications to the source code.