When typing code and i'm above 50 lines, or simply exceed the code window size, when press the down button on the scroll bar it doesn't ovey, just clic, and return to same position. Pressing up button doesn't make any error. Even when scroll code area shakes.
The editor is one of the weak points of SQLYog. I'm desperately hoping that the next major version has a new one.
To work around your problem, go to the last line you can get your cursor on and then hit return. This should cause the editor to work again. (at least it does for me when I run into this problem.)