I work on Windows with Cygwin. In Eclipse, I can do SVN checkouts and updates with the SVN on our server, which is running SVN 1.4.x. I'm doing this with the latest Subversive and connector. I've been told that after SVN 1.4.x, the "storage format" changed, so doing checkouts and updates with a SVN client newer than 1.4.x would screw up the .svn directories.
In fact, I think I've seen this happen. I tried doing an update with my SVN command-line client (I appear to have SVN 1.5.7, from CollabNet), in a project that I work on in Eclipse, and when I refreshed my Eclipse, it got so confused I eventually had to create a new workspace. Working in the old workspace gave me constant error dialogs from Subversive. I suppose it's possible this wasn't a storage format issue, but simply an issue with updating the SVN state outside of Subversive. I don't know. I don't attempt checkouts or updates from the command line anymore. Doing "svn diff" or other information queries works fine. Is there a SVN command-line version that would be "safe" to use for checkouts and updates that won't screw up my .svn tree or Subversive? I asked about this on the Subversive forum, but I'm having trouble getting a response.