Junctions?
What do you mean exactly?
Junctions are the NTFS equivalent of symbolic links. With these you can have i.e. a folder containing all roms/movies/etc. from all your hard drives in a single place; or you can replace a non-movable folder (Quicktime cache, browser cache, etc.) with a junction to a folder on another drive... You can find some information on
http://en.wikipedia.org/wiki/NTFS_junction_pointI use KillCopy to create them as WinXP comes with only a command line utility (fsutil.exe) to manipulate such links. There are some other alternative programs available as well - NTFSLink, Junction Link Magic and others.
The rebuilder reads files (or files within an archive) from a given source, checks the hash values against the database and creates any found match of it in the destination and uses the correct naming. If you got "remove rebuilt files" enabled, it deletes the file from the source (archive) and if the archive or folder is empty after this it gets removed, too (however there is a rebuilder advanced option which allows you to remove empty folders or not).
I am aware of the "Remove Matched Sourcefiles" and "Remove empty sourcefolders" options, and i use them when appropriate. The issue surfaces if there are junctions in the source - they get removed regardless if they point to an empty folder or to a folder full of roms. So, if i go through several CMP profiles and rebuild from that source, only the first one would receive the matched roms from the junction folder.
I noticed something which may be related - the properties of a folder containing a junction don't count the junction target in size calculation. Here is an example folder structure:
C:\ROMsC:\ROMS\FBA_roms < a junction to
D:\FBA\ROMsNow, if you right-click C:\ROMs and select "Properties", it would show 0 in the "Size" field (Windows Explorer bug?).
If you do the same for C:\ROMS\FBA_roms it would properly show the size of the D:\FBA\ROMs folder.
Maybe Clrmamepro is affected by the same bug and considers the junction as an empty folder, so it is removed when the above two options are enabled.
HTH