You're right, I just removed and added Update Manager and was given the option to change repository path from default.
I changed it to D:\VMware Update Manager\Data, but after finishing install and restarting the server folders were created in C:\VMware Update Manager\Data.
Anyway, after moving the folders to d:\, changing the <patchstore> tag and rebooting the server everything seems to be fine.
Thanks,
Ole Thomsen