Every startup of MyEclipse6.5M1 on vista will open 2 security-check-dialog :
regedit /e
"C:\Users\***\AppData\local\temp\jx_registry***"
"\HKEY_LOCAL_MACHINE\SOFTWARE\MOZILLA.ORG\GRE"

Can you go to MyEclipse > Installation Summary > Installation Details and paste the information here for me.

Are you working on 64 bit vista ?

Did you setup MyEclipse using the All in One installer ?

i am working on 32bit vista and setup with the all in one version here is my Installation Summary :

** System properties:
OS=WindowsVista
OS version=6.0
Java version=1.5.0_14


*** MyEclipse details:
MyEclipse Enterprise Workbench
Version: 6.5.0 Milestone-1
Build id: 6.5.0-M1-20080502


*** Eclipse details:
MyEclipse Enterprise Workbench

Version: 6.5.0 Milestone-1
Build id: 6.5.0-M1-20080502




Eclipse Platform

Version: 3.3.3.r33x_r20080129-_19UEl7Ezk_gXF1kouft
Build id: M20080221-1800


Eclipse RCP

Version: 3.3.3.r33x_r20080129-8y8eE9UEUWI6qujeED0xT7bc
Build id: M20080221-1800


Eclipse Java Development Tools

Version: 3.3.2.r33x_r20080129-7o7jE7_EDhYDiyVEnjb1pFd7ZGD7
Build id: M20080221-1800


Eclipse Plug-in Development Environment

Version: 3.3.3.r33x_r20080129-7N7M5DQVIA_6oJsEFkEL
Build id: M20080221-1800


Eclipse Project SDK

Version: 3.3.3.r33x_r20080129-7M7J7LB-u3aphGW6o3_VmiVfGXWO
Build id: M20080221-1800


Eclipse Graphical Editing Framework

Version: 3.3.2.v20080129
Build id: 20080221-1602




Eclipse startup command=-os
win32
-ws
win32
-arch
x86
-showsplash
-launcher
C:\Applications\MyEclipse 6.5M1\eclipse\eclipse.exe
-name
Eclipse
--launcher.library
C:\Applications\MyEclipse 6.5M1\eclipse\plugins\org.eclipse.equinox.launcher.win32.win32.x86_1.0.3.R33x_v20080118\eclipse_1023.dll
-startup
C:\Applications\MyEclipse 6.5M1\eclipse\plugins\org.eclipse.equinox.launcher_1.0.1.R33x_v20080118.jar
-exitdata
e7c_cc
-vm
C:\Applications\MyEclipse 6.5M1\jre\bin\javaw.exe

Eclipse 3.3 (still) sort of requires you to turn off UAC, or select 'Run as administrator' from the shortcut context menu. Yeah, UAC is great :-], but not for developers
And Eclipse 3.3 platform is not sufficiently 'fixed' to run properly on any type of Vista, so better install MyEclipse on top of Eclipse 3.4 RC1 (Not supported nor very compatible) or wait for MyEclipse 7.0, or run a VMWare Server or VirtualBox (both free) image with WIndows XP (not free) and install MyEclipse in the Virtual machine.

HTH
Ton