On of our support guys was saving .exe files to a win 7 desktop. When the action completed the file was missing.
When he disables Host IPS in the HIPS UI the .exe saves without issue.
Is there an option in the IPS list that can be disabled to stop this happening? I've had a look but have no idea what I'm looking for.
You need to look through your Host IPS signature violations (locally in the Activity log, or via ePO console). Sounds like an IPS signature is preventing WRITE operations on these files.