It is strange, though I am not even sure what works and what not.
Can you confirm that OSCDIMG made .iso's work and MKISOFS made ones do not?
Maybe it is an issue with file position (if this is the case then the Wimboot has a bug, minor as you want but still a bug).
Mkisofs has however an option to write files with a given "priority", in case.
You need a tool like isobuster (or similar) to find the actual file extents and compare them, but before that, have you tried some varations of the mkisofs command?
I mean, right now you have the -R switch (that will create a RockRidge directory structure) in one of the two commands and -J -joliet-long on the other (which will create a Joliet directory structure) whilst the:
oscdimg -h -n -betfsboot.com ISO %isofilespec%
seems like "as plain as possible" (maybe it has just a lower isolevel directory structure).
Does the issue appear with just BOOTMGR and \boot\BCD (or their EFI counterparts) or is the boot.wim involved?
(of course if there is a "fake" boot.wim the bootmgr will give an error, but it would be useful to understand if the Wimboot rror hapens before the bootmgr runs or
Can you post a set of commands that work (making use of oscdimg) and a set of commands that do not work (making use of OSCDIMG or MKISOFS)?
What works is the original MM buildpe.cmd script that only runs under WAIK. It uses that ultra simple oscdimg command line I posted before. It works just fine in all respects with 32 and 64 bit images.
What doesn't work is any version built with QuickPE or QuickRE (selecting an RE not a PE build).
I cannot confirm that all ISO's made with oscdimg work (and those made with mkisofs do not). I replaced the mkisofs with oscdimg in the makeISO.cmd script (not shown in code above) with the simple set of options / parameters used by MM's buildpe.cmd script but it too failed to boot with wimboot (it booted just fine from the USB key directly tho).
As for the mkisofs switches used in the makeISO.cmd script, they are exactly the same as in QuickPE version 0.9.3. I think the reason for the Rockridge vs Joliet options are due to issues erwan.l had with UEFI support. That is the distinctive difference between the 2 mkisofs lines, one is for EFI the other for BIOS..
As for when the error occurs, it is after grub2 loads the PXE wimboot. The error is reported by the wimboot code when it attempts to load the (boot.wim / sdi / bcd) files.
I have already posted the oscdimg commands that do work, and the mkisofs options that don't in my last post. HOWEVER, please be aware that the files and folders in the source ISO are quite different, and my gut tells me that's where the issue lies, and I suspect it lies in the boot files or folders ([BOOT] or the folders under BOOT).
Not sure what you mean by "extents", but if you explain that and what to compare using ISObuster I can scrutinize the ISO contents more carefully. Particularly with a focus on the boot files in the ISO structure.