The only other things that come to mind immediately to check are pretty obvious (forgive me for pointing them out; I understand you have probably tried this stuff):
1) under the Advanced tab of WS-Ftp, make sure you have Passive Mode checked - that is the default setting. That may be your problem - maybe it somehow got unchecked.
2) If one machine is fine, and the other is flaky, don't forget line condition can cause trouble - double check all connections, cables, etc.
Sorry it's not much, but I did want to make sure you checked both of those items.