I have a VisualStudio 8 project that builds fine under SE, but when I compile a single file in SE (13.0.2) I get two conflicts with the pch.
First off, my project is built with the "/Zc:wchar_t-" flag. It appears that compile.e will add "/Zc:wchar_t" if the option is on, but does not explicitly add "/Zc:wchar_t-" when the option is off, as it is in mine. The compiler, on the other hand, seems to assume it is on in the absence of any flag.
The second problem is that visual studio seems to add "/D _VC80_UPGRADE=0x0710" to the command line, even though that is not in the .vcproj. This is something that happens when a project in upgraded from VS7.1. In any case, SE is not adding the define, and that causes a PCH conflict when compiling a single file.
I have already "patched" my SE to fix these, but would be interested in a real fix when it is available.