On an intranet samba should be fine, as long as your shares are configured correctly, prehaps by either restricting the ip's that are allowed to connect to shares or using share authentitication with a different username and password to the rest of your machines.

As for your flash drive format it again in windows using a fat file system and you should have no problems using it on both pc's, my flash drive works like a charm on Fedora Core 2, I have set it to auto mount when ever i plug it in and have no problems loading it on any of my windows boxes, you should also check your /etc/fstab and make sure there is an entry along the lines of:

/dev/sda1 /mnt/flash auto user,noauto,kudzu 0 0

Hope this helps.