Nios2 errors compiling through samba share

Hi, I have a windows machine where I installed Red Hat Enterprise 4 on VMWare.

I have installed nios2 in both windows and linux. The main reason for using Linux is that it is over 6 times faster to compile the project!

The project is in a samba share in my windows hard drive, mounted on the linux system (all in the same machine on vmware). So I can compile the project using Linux Nios ide (version 6) and use quartus in windows to program the target board. And I can use my windows source control tools as the source tree is still in the windows hard drive.

It all works great, about 50% of the times it all compiles fast and without problems. But sometimes I get an error which looks like some timeout problem when compiling one of the source files (not always the same one). The error is:

/mypath/mysourcefile.cpp:560: fatal error: closing dependency file obj//mypath/mysourcefile.d: Input/output error

Just trying again ends up working fine, but it is very annoying. If anyone could give me any hint on how to impove things it would be much appreciated!

Thanks!