I have an idea of what might be happening, so please read fully and don't skip, because it might help.
Many cloning software are very temperamental and often try to "see" what is the host PC, controllers etc to get the best clone.
Are you cloning on a bench PC? As in, not the customer PC but a PC you use for technical tasks? If so, stop doing that unless you have a generic environment that you can safely clone in.
If you are cloning on the client PC, have the source drive connected via USB. It removes the drive as a possible boot device that may push flags in BIOS or EFI that your cloning software may determine for what partition map is needed.
Also if on a client system that supports legacy vs UEFI, make sure you clone in the mode your final install will be. In other words, don't change the system config just so your tools will boot. Make sure you have versions of your tools that will boot regardless of BIOS, EFI, SecureBoot etc.
Do you use the basic or "home" version of Macroum or Acronis? Just as a friendly reminder, they are not licensed for technician use, and don't perform the same as the higher editions. The higher workstation class products have way more features, and often have a fully licensed WindowsPE that the cloning runs from. They have options like crazy to make your life easier and allow you to control the clone.
Did I hit the nail on anything or maybe I'm off the mark? I've struggled before too, so I recognize some of this.