I have one 34" screen that I've virtually split into 2 vertical screens, with single taskbar (i.e. Taskbars disable in the monitor configuration).
The main monitor works great, but when I open application in the second monitor in full screen mode its lower part is hidden by the taskbar

DisplayFusion Pro 9.9
Windows 10 (20H2) (10.0.19044.0)

Sure - I'm attaching the file

Let me correct myself - the issue occurs when I split the monitor to 3 parts:
Left side: 1720*1440 ; Right side: 1720*940 and under it 1720*500
The taskbar issue occur with the 1720*500 split and I observe it with WhatsApp application - where the text bar for "Type a message" is hidden behind the taskbar
The issue occurs during DisplayFusion startup (reboot doesn't help)
I recently had to reinstall the Windows with all applications and it started since then

I've notice it also happens with Microsoft Teams (those are the main 2 applications I use in the Virtual display #3)
I think it happens also with other applications such as Chrome, but its mostly pops up when there is a text bar or menu at the bottom of the application (like in Whatsapp and Teams)

I tried it - but it doesn't seems to make any difference.

Sure - I attached the file

Looks like it was resolved with you advise to increase the height.
I played around with the numbers and 560 also works well.

Thank you for your support!