There could be a problem if you have more than one tab. The first tab uses how many pixels you set that option to, but the second and third and so forth take the previous heights of all the tabs, the separation, and how high to start and adds them all together for a new pixel location. If one was in % and not px it will throw the rest off.
Here is the file that contains that setting though:
\wp-content\plugins\wp-flybox\body_import.php
It starts on line 60 and ends on line 91.
Before you try the below, backup your file.
Only if you have 1 tab then you can replace line 60-91 (everything between “//wrapper” and “//filler” with this:
echo '<div class="wp-flybox_tab" id="wp-flybox_tab'.$i.'" style="pointer-events:all;width:auto;display:inline-block;overflow:hidden;position:'.$wpflybox_position.';border:0px;'.$right_or_left.':-9990px;top:XXXXX;z-index:999'.$i.' !important">';
Replace XXXXX with your height to start and type like 20px
or 25%
.