Got there in the end. Here is the proof I used, I thought I'd post it as it was quite fun to prove in the end. I would also appreciate it if anyone can point out errors. Also, apologies for poor presentation I'm fairly new to Latex.
Since [itex]q | F_{k} = 2^{2^{k}} + 1[/itex] [itex]\Leftrightarrow[/itex] [itex]2^{2^{k}}\equiv -1[/itex] (mod [itex]q[/itex])
Noting that [itex]2^{2^{k}} - 1 = (2^{2^{k-1}} +1)(2^{2^{k-1}} - 1) = F_{k-1}(2^{2^{k-1}} - 1)[/itex] you can write [itex]F_{k}[/itex] as:
[itex]F_{k} = 2^{2^{k}} + 1 + (2 - 2) = 2^{2^{k}} - 1 + 2 = F_{k-1}(2^{2^{k-1}} - 1) + 2 = F_{k-1}F_{k-2}(2^{2^{k-2}} - 1) + 2 = F_{k-1}F_{k-2}...F_{2}F_{1} + 2[/itex]
So for any [itex]l =1,2, ..., k-1[/itex] we can write [itex]F_{k}[/itex] as:
[itex]F_{k} = F_{k-1}F_{k-2}F_{k-3}...(2^{2^{l-1}} - 1) + 2[/itex].
Assume that for some [itex]l =1,2,...,k-1[/itex] we have [itex]2^{2^{l}}\equiv 1[/itex] (mod [itex]q[/itex]), then [itex](2^{2^{l-1}} - 1) = 0[/itex] (mod [itex]q[/itex]) and [itex]F_{k} - 2 = 0[/itex] (mod [itex]q[/itex] ) [itex]= F_{k}[/itex] since [itex]q | F_{k}[/itex]. So [itex]2|q \Rightarrow q=2[/itex], but [itex]F_{k} = 2^{2^{k}} + 1[/itex] is odd, so we have a contradiction. Thus [itex]2^{2^{l}} \not \equiv 1[/itex] (mod [itex]q[/itex]) [itex]\forall[/itex] [itex]l = 1,...,k[/itex] since also, already shown that [itex]2^{2^{k}}\equiv -1[/itex] (mod [itex]q[/itex])
Now, since [itex]q[/itex] is prime, using Fermat's Little Theorem [itex]2^{q-1} = 1[/itex] (mod [itex]q[/itex]) since [itex]q \not |[/itex] [itex]2[/itex].
Also,
[itex]F_{k+1} -2 = F_{k}F_{k-1}...F_{2}F_{1} = 0[/itex] (mod [itex]q[/itex]) since [itex]q | F_{k}[/itex]. So [itex]2^{2^{k+1}} + 1 - 2 = 0[/itex] (mod [itex]q[/itex]) [itex]\Rightarrow 2^{2^{k+1}} = 1[/itex] (mod [itex]q[/itex])
Noting that [itex]x^a \equiv 1[/itex] (mod [itex]m[/itex]) and [itex]x^b \equiv 1[/itex] (mod [itex]m[/itex]) [itex]\Rightarrow x^{gcd(a,b)} \equiv 1[/itex] (mod [itex]m[/itex]), we get the result:
[itex]2^{gcd(q-1,2^{k+1})} \equiv 1[/itex] (mod [itex]q[/itex])
Now, since [itex]gcd(q-1,2^{k+1})[/itex] must be a divisor of [itex]2^{k+1}[/itex] it must be of the form [itex]2^{l}[/itex] for some [itex]l=0,...,k+1[/itex] , but it can't be any [itex]l = 1,...,k[/itex] since otherwise [itex]2^{2^{l}}\equiv 1[/itex] (mod [itex]q[/itex]) contradicting our earlier result. Also, it can't be [itex]2^{l=0} = 1[/itex] since otherwise [itex]2^{gcd(q-1,2^{k+1})} = 2 \equiv 1[/itex] (mod [itex]q[/itex]) [itex]\Rightarrow q = 1[/itex] which is a contradiction, because [itex]q[/itex] is prime.
So, therefore, having exhausted all other possibilities, [itex]gcd(q-1,2^{k+1}) = 2^{k+1}[/itex], finishing the proof.