That's ok, i found the problem a couple of days ago. It was specifically to do with a Custom action running at Uninstall time.
Based on Powershell - example below. This has been disabled and the uninstall is working normally and leaving new custom files alone now.
Thanks for your help.
# Get APPDIR from AI and store
$InstPath = AI_GetMsiProperty APPDIR
# Set up variables for file tranfer
$Capture = Join-Path -Path $InstPath -ChildPath "Capture"
Remove-Item -LiteralPath $Capture -Force -Recurse