That's not exactly a typical problem with link.exe. First make sure that you have the "whole program optimization" feature turned off, the /GL compiler option and /LTCG linker option. If that doesn't help you'll need to gather some evidence that might pinpoint the source of the problem. SysInternals' ProcMon.exe utility is good for that.
If that doesn't help, check if this happens on another machine as well so you can eliminate some environment cause (like a virus scanner). If that doesn't help, you'll probably need the help from Microsoft Support. They'll need your project to troubleshoot the problem, you'll get your money back if it is a MSFT bug.