Starting with beta 5, all compatibility options are turned off by default.
Turning each compat options forces PEBakery to emulate WinBuilder's bug/quirk, or turn off new features.
Since Win10PESE, Win10XPE is designed with WB082, they require several compat options being turned on.
To be short, create PEBakery.ini (in the same dir where PEBakeryLauncher.exe exists) and put these lines in section [Compat].
[Compat]
AsteriskBugDirCopy=True
AsteriskBugDirLink=True
FileRenameCanMoveDir=True
AllowLetterInLoop=False
LegacyBranchCondition=True
LegacyRegWrite=True
AllowSetModifyInterface=True
LegacyInterfaceCommand=True
IgnoreWidthOfWebLabel=True
OverridableFixedVariables=True
EnableEnvironmentVariables=True
DisableExtendedSectionParams=True
LegacySectionParamCommand=True
Then delete project temp directories, such as Temp and Target.
In next version, making PEBakery automatically provide appropriate compat options is planed (by detecting which project is being loaded).