So glad to hear you isolated the problem. It is somewhat disturbing to hear of undocumented board design changes on the fly &/or schematics not matching what's actually in the machine. That just makes troubleshooting that much more challenging. Unfortunately, this isn't the first time I've read about similar issues.
Can you elaborate on what is defective in the fuse holder itself (like the fuse end contact points, or where it mounts to board, or internal crack somewhere embedded in the fixture.... etc).
How did you ultimately diagnose? I assume with a known good fuse in place it should have nil resistance across it, but for example does it act buggy only at higher current rate?