Hi Ana,
We ran into a similar problem and concluded it was due to the large file size of TUB #39. It takes a long time to load, and it took a couple of attempts on our side before we got it working, too. We had never seen this problem before (that I recall) until update #39.
Have your BASIS resource go into your BSI 10.0 server folders and view the log files for #39. They may need to try loading it again. As they keep refreshing the folder, hopefully they will see the log file size increase as it updates. Once the file size stops increasing (after several minutes), the update is complete and hopefully you will see update #39 reflect in BSI and in SAP.
Good luck!
Jay