How do all, hoping to save myself some trouble I've been having:

Running the original baldur's gate saga from the basic gog install so no tacked on mods.

I've tried to be vague to dodge spoilers but here's a bit of background.

Picked up Yeslick from the mines without issue, travelling over a fair proportion of the map and completed all the side quests I could find with him. But after first successfully clearing out the iron throne base on the top floor, he hit a glitch where he leaves and then chases the party to rejoin in a loop. I eventually abandoned him on the first level of the building. Fast forward a bit in the story when I have escaped from prison and exploring the sewers...found a set of stairs which led back up into the iron throne building...Yeslick was waiting to pounce.

Is there any way to fix this? Just running for the exit isn't as easy as before because the Flaming Fist are after me and I don't want to drop my reputation any more after killing one in my get-away. Also, he has the boots of speed so trying to run away from him is a pain. I know there was an issue with Yeslick in cloakwood mines, but I'm so far ahead of that and explored everywhere left on the map with him, I don't understand what tripped it off.

Anyways, any help would be much appreciated!

Did you flood the mines? You have 5 days in which to flood the mines after picking Yeslick up, or he will leave. Also, do you have Kagain in your party? Those two may eventually clash and fight.

Thank you for responding!

I was unable to flood the mines - I tried following the instructions but something got in the way, I forget what exactly. But it is well passed 5 days; I've gone on to clear Durlag's tower down to the warden level, went north up to Urgoth's Beard through the beasts, dealt with the river witch, wailed on some undead, explored all through the Gate and some of the sewers sections, the trading post and finally got to the Iron Throne with a lot of rest spamming to heal up.

If this is the answer though, and it was just a delayed response, is there a way around it?

Yes. Set the global variables for having flooded the mine within the five days. Open the console and type:

CLUAConsole:SetGlobal("MineFlood","GLOBAL",0)
CLUAConsole:SetGlobal("Flooded","GLOBAL",2)

You, sir, are a gentleman and a scholar, thanking you kindly for the massive help!

Glad I could help.