When opening a file from the command line while notepad++ is already running, notepad++ tries to open the file relative to the old current directory.

Repro:

2 directories

From commandline,
mkdir \dir1
cd \dir1
notepad++ file1.txt
mkdir \dir2
cd \dir2
notepad++ file2.txt

Save file2.  File2.txt appears in \dir1 instead of \dir2

http://blogs.msdn.com/oldnewthing/archive/2007/06/29/3594231.aspx