The scanner tree window is not empty, until the scan that eventually reports none missing but that can take 2-3 rescans to reach.
I think you may be confused regarding what I'm reporting though, there is no rebuilding or fixing occurring over these scans (i.e. all Fix options are disabled, and the scans are run back to back without rebuild runs in between or other changes to the files). The initial rebuild seems to create a complete set. The scans then make no changes to the files, but report fewer missing ROMs with each repeated scan until there are none. Repeating a new scan typically then shows missing ROMs again, but a different number than reported previously.
For example, I just reran "New Scan" on the set four times (again with all Fix options off, and no changes occurring to the files between runs). First run reported 466 missing ROMs, the second reported 613, third 550, and the fourth 452.
I've attached the requested items. I couldn't find an option to export the Scan Results window content, but included screenshots of the end of run 3 and 4's contents. Related ROM files can be pulled from:
https://archive.org/details/Sharp_X68000_TOSEC_2012_04_23Regarding the rebuilder, it will normally error fewer times than the scans do. On this set only ~50-70 failed adds vs the hundreds of missings reported by scan, similar to the scan the specific files and their number seem to change with each run. I'd guess the issues may be related though, in that both are failing to pick up on ROMs that are in place.