Ok, after further testing, I see it now. It has to be a small script to be noticeable. Most my scripts are hundreds of lines or longer, and at that size, no noticeable difference is there between this app and any other app which is why I couldn't see it originally. However, when under 150 lines or so, it can be seen. So this only appears when looking at short scripts and the amount of space is dependent on the number of lines as smaller scripts have a larger gap than larger scripts -- compare a 50 line script with a 150 line script, for example.
And just for more information, a small script on 6.35 also exhibits this behavior when I tested that. And once again, the larger the script, the smaller the space until around 150 or so lines, it becomes unnoticeable. So it's been that way since at least 6.35 and isn't a recent change in case that's helpful for Khaled.
I think you're being distracted by the symptom and not looking at the cause. The bug[*] is simple: it's impossible to scroll to the last line of text in the editor using the scroll bar, mouse wheel, or down arrow if the last line is blank (which, it usually is, since mIRC automatically puts a newline after the last non-blank line). Although you can get to it by using right arrow at the end of the last non-blank line.
[*] I think this might be intentional behavior.