This patch is no longer necessary with NSIS 2.45 and up
I have posted a patch for NSIS which fixes the issue in the upcoming Windows 7 Release Candidate (as well as build 7057 / 7068 / 7077 which were leaked early) where it would trigger a Program Compatibility Assistant warning. Only makensis.exe is altered... just replace it in the NSIS program directory. The updated manifest.cpp is included so you can build it yourself, too.
Download NSIS 2.44 Windows 7 Patch 1 by PortableApps.com
Details on the bug are posted in this NSIS issue: