[C DuDe]

uhhm,

Did you check if you have rearming set...think its the second icon from the right after the camera icon (I can't remember the name.. the one with the crew management in it).
Cause sometimes after ending silent running that icon stays off and you have to manually set it again otherwise the crew will not rearm your tubes.

I always do it manually even though its setup already.

Side note.
Might work the same way as the repair crew, when after sounding general courters you have to set your repair crew manually. If not... no one will work on the repairs.