Does any one know why this is happening and how to fix it? happends on both windows and linux boxes.

Yes, I have read the FAQ, and googled it.

The BOINC manager grabs about 95% of some files and then dies into a resume loop.
I noticed this ~2 days ago, I reset the project 24 hours ago, with no change except thet it restarted all downloads from the begining and hangs in the same place again.

It downloads many of the small support files and WU files okay, its just the new application ones.

A manual test using wget does the same thing:

"
>wget -c https://boinc.bakerlab.org/rosetta/download/rosetta_5.24_i686-pc-linux-gnu

--15:03:04-- https://boinc.bakerlab.org/rosetta/download/rosetta_5.24_i686-pc-linux-gnu
=> `rosetta_5.24_i686-pc-linux-gnu'
Resolving boinc.bakerlab.org... 140.142.20.103
Connecting to boinc.bakerlab.org|140.142.20.103|:80... connected.
HTTP request sent, awaiting response... 206 Partial Content
Length: 9,705,772 (9.3M), 424,092 (414K) remaining [application/octet-stream]

95% [+++++++++++++++++++++++++++++++ ] 9,281,680 --.--K/s

"