NO, Sameboxie is a sandbox program which executes other programs in an isolated area. It doesnt do anything to the exe file.
So i suggest,
1. throw away your AV,
or
2. just mark those files as exceptions,(every AV has feature like that now days,)
or
3. put those files in an archive like rar, zip, etc. The files will be detected but the AV wont do anything to the archive file.(it will be annoying to see warning msg again and again).
Anyway, i recommend not to use any AV.