It's very odd - I thought at first it might be my USB drive being corrupted - so I ran multiple chkdsk's - and after "reinstalling" the updater beta tonight, I get the same errors - when i click on abort update, obviously it ends the program, but when I click no to close the updater, it says that the MD5 checksums of (insert any program here) do not match - your download may have been corrupted. Package (insert any path and *.paf.exe deleted.) any ideas as to why this is happening - or has been happening for quite some time?
You're speaking about the current Beta release of the updater in the forums, which does have this issue. The download issue is due to a SourceForge.net issue. The MD5 error is a bug. You can report on it and ask about it in its current topic here:
https://portableapps.com/node/16779
A new release is coming shortly that should fix this.
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