This is most likely due to the default IS behavior of reusing FTP sessions when connecting to the same FTP server form the same user. If an error occurs during an FTP session and FTP logout is not called, then the FTP session remains in memory. Subsequent FTP activity will use this (stale) session, which typically exhibits the behavior you’re reporting. For example, the current dir may already be the directory you’re trying to cd to, thus the not found error.
For 6.1 there is a fix available. It’s Fix23 but I’m certain it has been subsumed by subsequent fixes. Contact support to get the fix. The fix lets you force new sessions and has a background thread that cleans up any stale sessions.
HTH
#webMethods#webmethods-Protocol-and-Transport#Integration-Server-and-ESB