Hello,
Check out SQLyog 4.0 BETA 2.
Apart from various bugfixes of BETA 1 (including the bug reported by you), it has got a new and improved SQL Editor. Now you can edit large SQL files without noticing any performance degradation.
For more information visit: http://www.webyog.com/forums/index.php?act…st=0&#entry3674
Eagerly waiting for your comments.