I think that the following patch may be sufficient to fix this:

<verbatim>
--- src/file.c
+++ src/file.c
@@ -244,10 +244,11 @@
 ** Convert to just /
 */
 void file_canonical_name(const char *zOrigName, Blob *pOut){
   if( zOrigName[0]=='/'
 #ifdef __MINGW32__
+      ||
       || (strlen(zOrigName)>3 && zOrigName[1]==':'
            && || zOrigName[2]=='/'))
 #endif
   ){
     blob_set(pOut, zOrigName);
</verbatim>

I will strive to boot up a copy of windows this afternoon and try it out.
In the meantime, a work-around might be to use forward slashes ("/") instead of
backslashes ("\") in the pathname, at least for the first character of
an absolute pathname.