I finally found something (btw the test I've send did not reproduce the bug,
if you set the same fapl in both file creation/open there is no problem).

My application runs correctly with the following patch, please let me know
if this shows an actual problem or if its related to my own application...

I was tracking the fc_degree, which was changing at insertion time in H5Fsfile.c
and then was leading to an error in H5F.c/H5Fopen/H5F_open). I found the
fc_degree was not updated in H5F.c/H5F_new, which was the caller of 
5Fsfile.c/H5F_sfile_add.

The brute force solution is to set the fc_degree at this place...
Again, I'm not able to write a test case reproducing the problem.
Anyway, my application now works ;)


--- src/H5F.c   2011-11-07 23:11:30.000000000 +0100
+++ src/H5F.c.modif     2012-05-24 17:28:06.000000000 +0200
@@ -832,6 +832,7 @@
 H5F_new(H5F_file_t *shared, hid_t fcpl_id, hid_t fapl_id, H5FD_t *lf)
 {
     H5F_t      *f = NULL, *ret_value;
+    H5F_close_degree_t  fc_degree;

     FUNC_ENTER_NOAPI_NOINIT(H5F_new)

@@ -949,6 +950,8 @@
            HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, NULL, "unable to append to list of 
open files")
     } /* end else */

+    H5Pget_fclose_degree(fapl_id,&fc_degree);
+    f->shared->fc_degree=fc_degree;
     f->shared->nrefs++;

     /* Create the file's "top open object" information */


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