Without seeing the code or setup in Spritebuilder it's difficult to diagnose. But it sounds like scaling it down may have left some aspects out of proportion.
For instance if you only scale the "core" down but not the sizes of the circle shapes that form the circumference, they will not have enough room next to each other to "relax" and those causing the joints to endlessly trying to resolve a collision situation that can't be resolved.
On the other hand if you make them too small, they will be able to snug under one another and basically can't hold the shape anymore.
You should enable physics debug drawing to see what is really going on and if you can post a screenshot of that and the setup in Spritebuilder I may be able to make some suggestions.
There's certainly no minimum joint size, but it does depend on the size of the bodies. For instance if the bodies of a joint are allowed to collide, and they are both circle shapes with radius 25, then the minimum theoretical distance for the joint is 25. Otherwise the joint would try to move both bodies closer than they possibly can, resulting in an unsolvable constraint that will result in an endless "fight" over which body takes precedence regarding its position. This adds additional forces to the physics simulation. It wouldn't surprise me that if a third body would touch either of the two jointed bodies, that it would be accelerated to much higher speeds than the simple collision would indicate.