"Disappearing" files/folders on SMB/CIFS network storage

I'm managing a vocational school's mixed network with a NAS using SMB/CIFS. I have now had some serious issues with Lion's finder up to 10.7.3: some files & folders simply disappear when dragged on there (i.e. they are set to be hidden). I have wasted a lot of time already trying to narrow down the issue:

- It's Lion only: the files are visible in any version of OS X prior to Lion & all flavors of Windows

- I tried deleting the various ._ that may affect file display

- I tried changing extended attributes settings in the commandline (i.e. chflags)

- finally noticed that it seems to only affect files that have the executable bit set when copied over. Huh?!?

(some files get saved with x set, some downloaded files (PDFs for example) have the executable bit set by default... again never a problem prior to Lion)

The fix for now is to change the permissions to chmod 644 (or 755 respectively), but since the networked volume doesn't handle changing permissions even as sudo from a client, I actually have to either use the cp command or enable show hidden files in the Finder, copy them on my desktop for example, change the permissions, and now when I copy them back, they will finally show up as expected. As you can imagine this is tedious & time-consuming, and most certainly not an option for our students & staff who have never seen the terminal (nor should they...)

Is this a know bug? Or a security "feature"? Has anybody else come across this? Any suggestions for a more permanent solution? It's not as bad as the Finder permissions issue in Snow Leopard that wasn't fixed until 10.6.4 and prevented us from upgrading for months, but it's still an upgrade stopper...