without something small to reproduce your error I can merely shoot in the dark.. but I'm lucky at this sometimes:)

Is the filhandle select -ed somewhere? Is fileno returning something meaningful just before the call to close? use diagnostics tell you something more?

It seems not be the case, but: is your handle a pipe open?

from open docs:

> If the filehandle came from a piped open, close returns false if one of the other syscalls involved fails or if its program exits with non-zero status.

There is something weird in the environment of the linux box? There are threads involved?

Also inspecting $^E can help at OS level

L*