In the project file, when the custom build step is called for Sylphis.i, it doesn't wrap filenames in quotes. I typically have stuff in folders with spaces, and without the quotes, most commands interpret the foldernames as multiple arguments, causing things to go haywire. :) Easy solution is to just wrap anything that looks like a filename in quotes. The following works fine:

"$(ProjectDir)\extern\tools\swig\swig" -Wall -c++ -python -I..\ -o "$(InputDir)\$(InputName)_wrap.cpp" "$(InputPath)"

Cheers