Assuming they're both set up with defaults, the problem might simply be that they're both trying to act as servers (windows uses a numbering scheme, with 20 as the the default for the master server, and 'os level 20' is also what samba tends to use as well, which means it's likely your two linux boxes are simply fighting each other, and if you have another MS windows server on the network, it's probably joining in on the fray as well. Your best bet is to go into your /etc/samba/smb.conf (or similar) file, and adjust one of the boxes to a lower OS level, which is easy if you read through the script.
Personally, though, if you're just running two Linux boxes, I'd opt for NFS, which is a whole lot easier to configure, more mature, more efficient, and less well understood by the script kiddies. It may take a couple extra minutes to read about and set up, but once you see it in action, you'll hate setting up SMB connections.