Cristiano pretty much summed up your issue but if I can I will add a few things that might help.
I wouldn't bother updating with your existing AutoPatcher release, there are so many outdated files you dont want to be
installing superseded patches - let's get your release Official.
First, if you notice in the image I have in post #1 it shows only XP SP3 (AutoPatcher Engine should always be present), so if you have
additional releases in the same \modules
folder of course the file count will not match. The .md5 files we are posting is for that
particular release only - it would be a pain to configure every possible combination of releases and provide an .md5 for the package.
If you feel up to it you could go through your release and remove a few files and folders incrementally (see Cristiano's spoiler list) don't
forget the text file I supplied, it also has the list of needed files for XP SP3 English, anything else can be removed. You also have the
option of downloading a new release - just remember to update it regularly and I would avoid more than 1(one) OS per folder. It isn't a
problem having the NET Framework in the same folder as XP SP3. In fact, if you want more than just XP you should say so and we can
advise on how best to download the releases.
The issue with updates being selected again after you attempted to install them can be a detection issue, but since the release is unofficial
and the patch may be outdated and long since replaced, lets get the release Official and if the detection issues are still present you should
post a list (starting a new topic would be best).
You shouldn't have to download files again and again but updates get replaced, folders get rearranged, new .apm files are needed at least once
a month (remember Patch Tuesday) so you can expect to run apup.exe a few times every month - but it is more to update and clean house not
to download the same files over and over.
According to the files mentioned in the pdf document all but one update is available in either the latest XP SP3 package or the NET Framework
Addon Pack. The only update I'm not finding is KB961118 - everything else seems to be available. Beware, the NET Framework package is large
due mostly to 3.5 - more than 230MB alone.
So, which is it - start fresh (the easiest way to get Official) or do some serious housecleaning?