There are two builds of NppExec: the Unicode build and the ANSI build. The Unicode build is compatible with Unicode Notepad++ and the ANSI build is compatible with ANSI Notepad++. You can check your version of Notepad++ by pressing F1 or from its main menu (? -> About Notepad++). You will see something similar to "Notepad++ v5.1.3 (UNICODE)" or "Notepad++ v5.1.3 (ANSI)". The corresponding version of NppExec (Unicode or ANSI) is required.
I recommend you to use Unicode version of Notepad++. The ANSI version of Notepad++ exists just for compatibility with old non-Unicode systems (such as Windows 98 or Millenium) and with old non-Unicode plugins.
Talking about NppExec, its Unicode build is more powerful because it has a full Unicode interface and supports ANSI, UTF-8, UCS-2 LE (Unicode wide characters in Windows) and UCS-2 BE input files. The ANSI version of NppExec supports just ANSI input files. It is caused by the following reason: conversion of UTF-8 or UCS-2 to ANSI may lead to loss of some Unicode characters which have no ANSI analogue.