I've noticed a bug with the short sword proficiency, namely my character (and Imoen) are not gaining the bonus to THACO and attacks per round when using daggers and short swords.

Does anyone know of a patch that remedies this? I've been trawling through the readme's of various fanmade patches but have not come across any mention of this bug.

I'm running the "vanilla" version straight from GOG with no other mods or patches installed.

There is no Short Sword or Dagger proficiency in vanilla BG1: the proficiency is 'Small Swords', which covers both. There is no bonus for proficiency in BG1, either. What proficiency does is to negate the penalty that is applied by NOT having proficiency in a particular weapon. Each slot negates the penalty by a pre-determined amount. There is no bonus to attacks per round, unless a weapon supplies it, such as bows or magical enchantments.