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My files are where they should be. I have discovered that all my software IS updating but I was expecting ticks to remain on the items updated in the left hand pane and they don't. I think they should really but they don't.  So, as per usual, the problem wasn't what I thought it was! At least my software is being updated but I have to check it, whereas if the items were still ticked, I would have more confidence that it was working. Still, you can't have everything, I suppose.  Here is my settings file - nothing amiss here:

#┬ÁTorrent
#360 Total Security
7-Zip
#8GadgetPack
#Adblock Plus for IE
#Adobe Air
#Adobe Flash Player
#Adobe Flash Plugin
#Adobe Acrobat DC
#Adobe Shockwave
#Advanced SystemCare
AdwCleaner
#AIMP
#Ares
#Audacity
#AutoHotkey
#AutoRun Organizer
#AVG
#Avast Free Antivirus
#calibre
#CamStudio
CCleaner
#CDBurnerXP
Chrome
#Classic Shell
#CMake
#CodeBlock
#ComboFix
#Copy Handler
#Core FTP LE
CPU-Z
#CrystalDiskInfo
#CrystalDiskMark
#Cybereason RansomFree
#DavMail
#Display Driver Uninstaller
#Discord
#DiskCheckup
#DOSBox
#Driver Booster
#Dropbox
#EditPad Lite
#EMET
#eMule
#Evernote
#FastStone Image Viewer
#FileZilla Client
#Firefox
#Foobar2000
#Format Factory
#Foxit Reader
#Free Studio
#Freemake Video Converter
#Frhed
#GIMP
#Git
#Glary Utilities
#GlassWire
#GOM Player
#Google Drive
Google Earth
#GPU-Z
#Greenshot
#HashTab
#Hotspot Shield
#HWiNFO32
#HWiNFO64
#HWMonitor
#iCloud
#Imgburn
#IrFanView
iTunes
Java 8 x64
Java 8 x86
#jetAudio Basic
#Kaspersky TDSSKiller
#KeePass
#K-Lite Mega Codec
#LibreOffice
#Logitech SetPoint
#Magic ISO
#Malwarebytes Anti-Virus
#Malwarebytes Anti-Exploit
#Junkware Removal Tool
#Media Player Classic
#MediaInfo
#MediaMonkey
#Microsoft Security Essentials
#MP3Tag
#Multi Commander
#MusicBee
#Nokia PC Suite
#Nokia Suite
#NotePad ++
#NoteTab Light
#OOShutup10
#OpenOffice
#Opera
#Origin
#ownCloud
#Paint.Net
Pale Moon
#PDFedit
#PDFsam Basic
#PDF-Viewer
#PeaZip
#PicPick
#Pidgin
#PNotes
#PotPlayer
#Process Hacker
#Process Lasso
#PureSync
#PuTTY
#qBittorrent
#Razer Cortex
#RDCMan
#RealPlayer Cloud
#Reg Organizer
#Registry Life
Revo Uninstaller
#RKill
#RougeKiller
#SamsungKies
#SanBoxie
#SFXMaker
Silverlight
#Simple System Tweaker
Skype
#Soft Organizer
#SMPlayer
#SonyPC
#SpeedyFox
#Spybot Search And Destroy
#Startup Delayer
#Steam
#Stereoscopic Player
#Subtitle Edit
#Subtitle Workshop
#SumatraPDF
#SUPERAntiSpyware
#SyncBackFree
SysinternalsSuite
#TeamViewer
#TeamSpeak
#Telegram
#TeraCopy
#Thunderbird
#TortoiseSVN
#Unchecky
Unlocker
#UPlay
#Viber
#Virtual Box
#Vuze
#VLC Media Player
Waterfox
#WhatsApp
#WhoCrashed
#WinAMP
#WinUAE
#WinDirStat
#Windows Repair
#Windows Repair Portable
#WinMerge
#Winrar
#WinSCP
#WinZip
#Wireshark
#Wise Care 365
#Wise Folder Hider
#Wise Uninstaller
#Wise Registry Cleaner
#Wise Program Uninstaller
#WorldWide Telescope
#Yahoo! Messenger
#Zoner Photo Studio

I'm sure the problem is not app specific as none were (auto) selected at all. They all updated manually perfectly so it is the auto-select process that is not working. The file name referenced in the exe maybe or the need for a path even if in the same directory. A header for the settings file to tell the program what it is? I don't know. I'm sure others are using it perfectly well!

Just out of interest, my apps include CCleaner, CPUiD, Revo Uninstaller, Java and Adobe Acrobat DC. I am running Windows 7 Ultimate X64 with a core 2 Duo, SSD and 8 GB ram. (tried Win 10 - didn't like it!).

As I said, I don't think it's anything to do with the apps. It's the way I have PMPC & the settings file configured somehow. The file didn't download so I copied and pasted it into notepad and then saved it as a .settings file as per your instructions. I have a free version of PMPC and have therefore not had an activation email. Do I need one? Obviously it has to work before I can donate. It's a brilliant concept which nobody else has developed perfectly as yet, though there are a few triers.  Being able to add custom app entries and remove those not likely to be used, would help and also streamline it a Lot. I realise custom entries are problematic but with enough parameters it can work. Most of the existing code would still work. For me, as I reconfigure laptops and PCs as a hobby, it would save me having to explain to people how to install updates minus the unwanted invasive stuff. Anyway for now, I need auto-selection.

ps. I have downloaded again but the same thing happened. The common denominator is ME! Help.
Cheers

I have created the DefaultApps.Settings file in the same directory as PatchMyPC.exe and removed the # marks from my installed programs. I cannot seem to get PatchMyPC to auto-select. I'm sure I must be missing something as this is so fundamental. Is this a restriction of the free version, perhaps?
Cheers
DoubleHelixBluff
ps. I tried to attach a 56kb GIF but received  this error:
"The upload folder is full. Please try a smaller file and/or contact an administrator."