I know this is an old question, but I came across this when solving the problem myself. None of the answers here are quite perfect, and several of them have complicated caveats or will break on pathological layouts. Here is my solution:
Solve the board (forward, not backward) with unmarked tiles. Remove two free tiles at a time. Push each pair you remove onto a "matched pair" stack. Often, this is all you need to do.
If you run into a dead end (numFreeTiles == 1), just reset your generator :) I have found I usually don't hit dead ends, and have so far have a max retry count of 3 for the 10-or-so layouts I have tried. Once I hit 8 retries, I give up and just randomly assign the rest of the tiles. This allows me to use the same generator for both setting up the board, and the shuffle feature, even if the player screwed up and made a 100% unsolvable state.
Another solution when you hit a dead end is to back out (pop off the stack, replacing tiles on the board) until you can take a different path. Take a different path by making sure you match pairs that will remove the original blocking tile.
Unfortunately, depending on the board, this may loop forever. If you end up removing a pair that resembles a "no outlet" road, where all subsequent "roads" are a dead end, and there are multiple dead ends, your algorithm will never complete. I don't know if it is possible to design a board where this would be the case, but if so, there is still a solution.
To solve that bigger problem, treat each possible board state as a node in a DAG, with each selected pair being an edge on that graph. Do a random traversal, until you find a leaf node at depth 72. Keep track of your traversal history so that you never repeat a descent.
Since dead ends are more rare than first-try solutions in the layouts I have used, what immediately comes to mind is a hybrid solution. First try to solve it with minimal memory (store selected pairs on your stack). Once you've hit the first dead end, degrade to doing full marking/edge generation when visiting each node (lazy evaluation where possible).
I've done very little study of graph theory, though, so maybe there's a better solution to the DAG random traversal/search problem :)
Edit: You actually could use any of my solutions w/ generating the board in reverse, ala the Oct 13th 2008 post. You still have the same caveats, because you can still end up with dead ends. Generating a board in reverse has more complicated rules, though. E.g, you are guaranteed to fail your setup if you don't start at least SOME of your rows w/ the first piece in the middle, such as in a layout w/ 1 long row. Picking a completely random (legal) first move in a forward-solving generator is more likely to lead to a solvable board.