I can't upload after the fileserver crashed.

Sat 08 Jan 2011 01:53:51 PM PST	rosetta@home	[error] Error reported by file upload server: [t476__boinc_nmr_cm_rnd1_loopbuild_threading_tex_IGNORE_THE_REST_22840_1591_0_0] locked by file_upload_handler PID=-1
Sat 08 Jan 2011 01:53:51 PM PST	rosetta@home	Temporarily failed upload of t476__boinc_nmr_cm_rnd1_loopbuild_threading_tex_IGNORE_THE_REST_22840_1591_0_0: transient upload error
Sat 08 Jan 2011 01:53:51 PM PST	rosetta@home	Backing off 1 hr 20 min 50 sec on upload of t476__boinc_nmr_cm_rnd1_loopbuild_threading_tex_IGNORE_THE_REST_22840_1591_0_0
Sat 08 Jan 2011 01:58:45 PM PST	rosetta@home	Started upload of t476__boinc_nmr_cm_rnd1_loopbuild_threading_tex_IGNORE_THE_REST_22840_1591_0_0
Sat 08 Jan 2011 01:58:46 PM PST	rosetta@home	[error] Error reported by file upload server: [t476__boinc_nmr_cm_rnd1_loopbuild_threading_tex_IGNORE_THE_REST_22840_1591_0_0] locked by file_upload_handler PID=-1
Sat 08 Jan 2011 01:58:46 PM PST	rosetta@home	Temporarily failed upload of t476__boinc_nmr_cm_rnd1_loopbuild_threading_tex_IGNORE_THE_REST_22840_1591_0_0: transient upload error
Sat 08 Jan 2011 01:58:46 PM PST	rosetta@home	Backing off 26 min 56 sec on upload of t476__boinc_nmr_cm_rnd1_loopbuild_threading_tex_IGNORE_THE_REST_22840_1591_0_0
Sat 08 Jan 2011 01:58:46 PM PST	rosetta@home	Started upload of t475__boinc_nmr_cm_rnd1_loopbuild_threading_cst_relax_tex_IGNORE_THE_REST_22838_1625_0_0
Sat 08 Jan 2011 01:58:48 PM PST	rosetta@home	[error] Error reported by file upload server: [t475__boinc_nmr_cm_rnd1_loopbuild_threading_cst_relax_tex_IGNORE_THE_REST_22838_1625_0_0] locked by file_upload_handler PID=-1
Sat 08 Jan 2011 01:58:48 PM PST	rosetta@home	Temporarily failed upload of t475__boinc_nmr_cm_rnd1_loopbuild_threading_cst_relax_tex_IGNORE_THE_REST_22838_1625_0_0: transient upload error
Sat 08 Jan 2011 01:58:48 PM PST	rosetta@home	Backing off 3 hr 43 min 4 sec on upload of t475__boinc_nmr_cm_rnd1_loopbuild_threading_cst_relax_tex_IGNORE_THE_REST_22838_1625_0_0
Sat 08 Jan 2011 01:58:48 PM PST	rosetta@home	Started upload of t469__boinc_nmr_cm_rnd1_cs_frags_loopbuild_threading_tex_IGNORE_THE_REST_22839_1747_0_0
Sat 08 Jan 2011 01:58:49 PM PST	rosetta@home	Project file upload handler is missing
Sat 08 Jan 2011 01:58:49 PM PST	rosetta@home	Backing off 2 hr 3 min 18 sec on upload of t469__boinc_nmr_cm_rnd1_cs_frags_loopbuild_threading_tex_IGNORE_THE_REST_22839_1747_0_0

There are similar reports in the Number Crunching forum. It is most likely caused by the server being overloaded after being offline for so long. I expect the problem will correct itself eventually, but you might want to keep an eye on the Number Crunching forum in case there is any further news.