I don't have exact data to hand, but I think the answer to your question is 'the early 1960s'. Hunter sqns were commanded by a Sqn Ldr and (we don't have the eXecutive Officer structure as such in the RAF) his 2 flight commanders would have been Flt Lts. The first Lightning sqns were commanded by Sqn Ldrs but these posts were soon upgraded to Wg Cdr (by about 1963 I think). V-force bomber sqns were, if I remember correctly, always commanded by Wg Cdrs. Once again, the 2 flights within such sqns were led by Sqn Ldr flight commanders.
Lower down the food chain (then...) helicopter sqns were commanded by Sqn Ldrs until No. 72 Sqn built up its Wessex numbers and was re-established to Wg Cdr in 1966. Whirlwind sqns remained under Sqn Ldr command until the type was replaced by Puma (in the TacSH world) with Wg Cdr bosses.
Hope that helps, and it should at least flush out the many facts I have undoubtedly got wrong.