I understand that you are referring to the filter in Object Browser? Please confirm.
It will display the first match (alphabetically) and I don’t think there is any change in this respect for the very beginning where we introduced this.
I realize that this is inconsistent with the behavior of auto-complete in the editor (where a match will only display when there is only one possible match). I think for most users current behavior is convenient, but if you have a lot of database objects in same level named with same initial letters (mydb1, mydb2, mydb3 etc.) you may experience what you describe.
Personally I agree that this could be implemented better. I have added an issue in our issuetracker at https://code.google.com/p/sqlyog/issues/detail?id=2037. We will discuss this.