well, of course I need a lot more information like which set in which dat is ignored....generally, if a file is not rebuilt, it's not matched against the current dat, i.e. crc32+size match (and md5/sha1 match as an addition). Also it might get skipped if it's locked by a different application. Batchrun uses its own rebuilder settings (if set, they overwrite the profile own ones) ...but generally batchrun is just a sequentially call of the single profiles...so maybe you should compare the rebuilder settings batch vs profile....
...on the other hand, if you're talking about network drives, that it could be related to an issue where (esp. Samba) got problems and skips files....however it's a network drive configuration issue and not cmpro related...