Hard to tell without a picture, but if it now runs well, plug the hole.............and ride it !
Gasket rubber sealant may be the answer - it's easy to get it off later if need be.....
Sounds like something's been left off after someone fiddled with it..............

 

Okay thanks, will post a piccy soon as i can as i am curious about it and why its been done. I suspect its been used as quick access to inject cleaner or similar....
Anyhow...

Rode it today in sunny dry hot weather with my new avons on and pure bliss. Started first time again. Happy days...