I have the same issue. Upgrading from db v. 3.1.0.0 to 3.3.0.5.
Script returns the following for all monographs:
[code: Installer Installer::migrateSubmissionCoverImages]
PHP Warning: copy(presses/1/monographs/1/simple/cover.jpg): failed to open stream: No such file or directory in /home/0/w45/beta/lib/pkp/classes/file/FileManager.inc.php on line 182
etc.
The file is in the files folder. Upgrade finishes with no further errors. But UTF-8 encoding seems to be broken (Scandinavian letters are corrupted) and all covers are missing.