A workaround is to change the mount command to add the noserverino,nounix options :

sudo mount -t cifs //SERVER/Bases/some/path ~/mnt/data -o user=windomain/login%password,noserverino,nounix

Florian pointed me to the right direction, that is the mdb_find_file function in the source code of the MDB tools :

static gchar *mdb_find_file(char *file_name)

{

    struct stat status;

    gchar *mdbpath, **dir, *tmpfname;

    unsigned int i = 0;



    /* try the provided file name first */

    if (!stat(file_name, &status)) {

        return g_strdup(file_name);

    }



    /* Now pull apart $MDBPATH and try those */

    mdbpath = (gchar *) getenv("MDBPATH");

    /* no path, can't find file */

    if (!mdbpath || !strlen(mdbpath)) return NULL;



    dir = g_strsplit(mdbpath, ":", 0); 

    while (dir[i]) {

        if (!strlen(dir[i])) continue;

        tmpfname = g_strconcat(dir[i++], "/", file_name, NULL);

        if (!stat(tmpfname, &status)) {

            g_strfreev(dir);

            return tmpfname;

        }

        g_free(tmpfname);

    }

    g_strfreev(dir);

    return NULL;

}

As I don't have any MDBPATH env var, it's obvious that there is an error in the stat call. I googled in that direction and got this :

http://www.linuxquestions.org/questions/programming-9/problem-with-stat-on-cifs-852983/

As I didn't try to recompile the MDB tools to get the error code, I'm not sure it's the same problem but adding the options that this thread suggested solved my problem, there's no more error when calling mdb-export.