The first installation of the new June update went well but locked up after a save. When I tried to restart my updated Arduino UNO REV3 V101 for the second time. I got a message from Windows XP that said the software has been disabled to protect your computer. After that I was never able to load the June updated arduino software. Oddly enough I went back to the earlier version arduino 100 and the software returned to normal and worked just fine. I am nonplussed by this action and have no idea as to what happened. Has anyone else experienced anything like this? Solutions are welcome, perhaps there is a bug in the new version or perhaps I had a mini brown out that knocked the software our. The new revision should have started after several computer restarts but it never came back. The earlier version will have to work for now.
Are you certain that was a Windows message? That sounds like anti-virus software (or a virus) that is preventing access to the program.
I am certain that message was not from Windows itself unless it was referencing DEP - Data Execution prevention. If it did mention DEP, take a look at this http://support.microsoft.com/kb/875352
I would guess there is a 99% certainty that the message is related to a third-party security application that has decided that the arduino.exe file is malicious software. Check whatever security software you have and figure out how to see the list of blocked applications.
You can also try booting into safe mode and see if it runs from there with the security software disabled.