If you are seeing a lot of these, then there could be another problem (like they are not getting deleted). They should only be on disk a second or two (depending on size) - and it takes being touched by some other process (Windows Indexing, manual scan, disk monitor, etc) to cause them to be detected again. It would help if we knew what process is causing the re-detection of these files.
The SEPM option - What to do when new definitions arrive - gets translated into this value in the Registry on the SEP client:
HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Symantec\Symantec Endpoint Protection\AV\Quarantine\DefWatchMode (exclude the Wow6432Node if 32-bir). The possible values are:
0 - Always rescan
1 - Repair only (and put repaired files back into Quarantine)
2 - Prompt (same as Rescan All in the Quarantine UI)
3 - Do Nothing
In the case of SMB, since SEPM does not offer the option - it may not reset the value every time a new policy is downloaded (but it might).
Another option is to exclude the specific folder used to rescan (Centralized Exceptions). You can do this from SEPM or on the client - but - this folder is deleted after rescan - and it must exist to create the exception on the client - create the folder, create the exception, then delete the folder. The foldername is:
ProgramData\Syamantec\DefWatch.DWH (or under user ApplicationData\Symantec in older OSs)..