As the data is binary, you shouldn't have to worry one iota about newlines, because you'll be treating it as binary data (use binmode on Win32). Don't try to read the file using <FH>; use sysread. In addition, this bit from the Storable documentation may be useful to you:

You can also store data in network order to allow easy sharing across multiple platforms, or when storing on a socket known to be remotely connected. The routines to call have an initial n prefix for network, as in nstore and nstore_fd. At retrieval time, your data will be correctly restored so you don't have to know whether you're restoring from native or network ordered data. Double values are stored stringified to ensure portability as well, at the slight risk of loosing some precision in the last decimals.