Can you make sure “Smooth Scroll” is NOT set in the Scroll page of configuration properties?
Which version of EmEditor did NOT have this problem?
Does the problem appear only with a certain file, or very large files?
If you still see the issue, I am not sure if I understand exactly what the issue is.
Can you send me a sample file (after zipped) at tech @ emurasoft.com as well as REG files (or INI files if you use EmEditor as portable version)? If you decide to send me REG files, you can export them at HKEY_CURRENT_USER\SOFTWARE\EmSoft in the RegEdit.exe, and zip before you attach the reg file.
Also, screenshots or screencast would help too.