When updating to 4.4.1 from 4.3.1 Softaculous ran without a hitch (no errors displayed) and I followed the instructions to navigate to the WHMCS folder to complete the installation for the script.
However when viewing the Admin panel the v4 theme appeared incorrectly (the left hand side menu was in the middle of the page and the main content of the page appeared below the menu)
I contacted support for WHMCS and they informed me that there had been a change to the templates and the best way to fix the error I was seeing was to manually download the 4.4.1 zip and re-upload the /whmcs/admin/templates/ folder contents and delete all files (apart from index.php) in the /whmcs/templates_c/ folder.
This solved the display error.
Thought this might be useful to someone but also potentially the Softaculous team if there's any way this can be fixed in the script.