Here's another way. Let $a_n$ be the number of sequences in $n$ tosses of a coin in which there are at most 4 consecutive outcomes of one kind. Then by simple counting $a_1=2$, $a_2=4$, $a_3=8$, $a_4=16$, and $a_5=30$. With a little thought you can get the recurrence relation $a_n=2a_{n-1}-a_{n-5}$ Now there are two ways you can go. You can just use this recurrence to grind out $a_6=2\times30-2=58$, $a_7=2\times58-4=112$, and so on until you get up to $a_{12}$. Or you can use standard techniques to solve the (homogeneous, linear, constant-coefficient) recurrence, but I think it gets messy for this one. Well, that's what computers are for!
EDIT: OP has remembered that the outcome is to be 6 heads and 6 tails, so the above is irrelevant. So let's do inclusion-exclusion instead.
We start with $12\choose6$. We subtract all the ways of having 5 (or more) consecutive heads. That's 56, because the first of the 5 consecutive heads can be in any one of 8 locations, and, once you've fixed the first of the 5 consecutive heads, you've got 7 remaining tosses, of which 1 is supposed to be heads. There are also 56 ways of having (at least) 5 consecutive tails; subtract those as well.
Now add back in all the ways of having two instances of 5 consecutive heads. The only way for that to happen is to have 6 consecutive heads, and there are 7 ways for that to happen. Similarly, 7 ways to have two instances of 5 consecutive tails.
Also add in all ways of having 5 consecutive heads and 5 consecutive tails. If the heads are 1 through 5, there are 3 places for the tails, and 2 ways to fill in the other two slots; if the heads are 2 through 6, 2 places for tails, 2 ways to fill; heads 3 through 7, 1 place for tails, 2 ways to fill, making 12 ways with the runs of heads preceding the run of tails; another 12 the other way around.
Now we have to subtract out all the ways that meet three conditions. By the way, if you're getting the impression that there's nothing slick about inclusion-exclusion, at least for this problem, you're right, but it's what the customer wanted, and we've come this far, so let's go for it. We can have 6 consecutive heads and (at least) 5 consecutive tails, 4 ways (heads starting at 1, 2, 6, or 7), or 6 consecutive tails and 5 (or more) consecutive heads, another 4 ways.
Finally, we have to add back in the 2 ways of meeting four conditions; 6 heads followed by 6 tails, or the other way around.
So the answer would appear to be ${12\choose6}-56-56+7+7+12+12-4-4+2$ whatever that is.
MORE EDIT: I figured out where I went wrong. In the next-to-last case, meeting three conditions, 6 heads and 5 (or more) tails can happen 6 ways, not 4. With the 6 heads starting at 1, the 5 tails can start at 7 or 8, and with the six heads starting at 7, the five tails can start at 1 or 2. Add in the heads starting at 2 or at 6 and you get 6 ways, not 4. This makes the final calculation ${12\choose6}-56-56+7+7+12+12-6-6+2$ which is 840, in agreement with everyone else.