I use SME 6 with Mac OS X (panther) and have experienced similar difficulties.
Another infuriating problem is when browsing the contents of an ibay via the Finder, the files and directories seem to disappear when you select them (most alarming the first time it happened!).
To resolve it, I've had to unmount the disk (or ibay) and remount, or use the Terminal. This is when connecting via AFP, so perhaps the solution is to connect using SMB as RayG suggested.