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I just freshly intalled Windows 98 in a VM and installed Autopatcher 2007 right away.
Now the boot animation is gone and during boot only a DOS prompt is shown.
Is there a way to fix that and bring back the boot animation?

Nevermind i found out how.
You need to navigate to a hidden file in the C: folder in Windows 98.
(first make hidden system files visible by navigating to View<Folder options<View (select tab) and check "Show all files and folders" under the "Filed and Folders" category.

Then navigate to C: and there will now be a once hidden file called "MSDOS.sys"
Open MSDOS.sys in notepad and scroll down to the very bottom.
There will be a value named "Logo=0"and its set to 0.
Set the value to "Logo=1" (without brackets) and save the file on the desktop as "MSDOS.sys" (again with no brackets).
Now rename the old MSDOS.sys file in C: to MSDOS.sys.old and paste the newly created MSDOS file from the desktop to C:

(WARNING: MAKE SURE TO FOLLOW THE STEPS ABOVE VERY CAREFULLY AS MSDOS.SYS IS A FILE CRUCIAL FOR WINDOWS TO START. REMOVING, WRONGLY EDITING OR RENAMING THE FILE INCORRECTLY WILL RESULT IN A BRICKED UP SYSTEM!!!!!)