Same result here but also get false on common files..
Excerpt from log file
Detection error for file C:\APUP\modules\Critical\__MSIE_critical\IE7-WindowsXP-KB2544521-x86-ENU.apm
MD5 Hashes do NOT match. Expecting A3EA70D478C654895A85A8E4EBB3F52C, but found 1ABDDCED2D413F519AE5B321CC196DB2!!!
MD5 Hash (525DE0AF0BB958F1C7D3D3FADB04D06A) Matches MSIE Critical APMs
MD5 Hash (0F383BDBFB52B91F5776705CF8924F67) Matches MSIE Critical APMs
Detection error for file C:\APUP\modules\Critical\__MSIE_critical\IE8-WindowsXP-KB2544521-x86-ENU.apm
MD5 Hashes do NOT match. Expecting D8F9F9E3BD99D91EC8F1CF7D95F05418, but found 685118F03A002126BF4B2BBFE1896D3D!!!
Detection error for file C:\APUP\modules\Critical\__MSIE_critical\IE8-WindowsXP-KB2618444-x86-ENU.apm
MD5 Hashes do NOT match. Expecting 13E5D2824C5C33751F2D7931A69FEC7B, but found 7F4D2A6EFAA920D133051F80E18F1F03!!!
Detection error for file C:\APUP\modules\Critical\__MSIE_critical\WindowsXP-KB2544521-x86-ENU.apm
MD5 Hashes do NOT match. Expecting 4F81C22E21574A73923DAD3F3BC88258, but found 9C93ACD574B6958E80C9287A3C25430B!!!
MD5 Hash (3A0E99D41355DDB10B5E552B447869EE) Matches MSIE Critical APMs
Item MSIE Critical APMs is missing or its parts are not completely downloaded. Adding whole download for this item to the queue.
--Adding
http://www.autopatch...l_20111213.7z--
Files to be Downloaded: 2
Estimated Total Download Size: 10,320
02/10/2012 11:47:13 | Download Thread 1 Will Download File: msie_enu_critical.7z
Download Thread 1 Problem Detected: Expected Size: 10K Current Download Size: 2K
02/10/2012 11:47:13 | Download Thread 1 Will Download File: windows_dotnet.7z
Download queue processed. Proceeding to next phase.
Download Error: C:\APUP\temp_bin\windows_dotnet.7z
File size does NOT match. Expecting 8242, but found 8186!!!
Download Error: C:\APUP\modules\Components\__dotnet\NDP20SP2-KB2539631-x64.apm_files\NDP20SP2-KB2539631-x64.exe
File size does NOT match. Expecting 15044496, but found 5167464!!!
***Processing Cleanup Routines***
Extracting. Command: "C:\APUP\apup_bin\7za.exe" x "C:\APUP\temp_bin\msie_enu_critical.7z" -o"C:\APUP\modules\Critical\__MSIE_critical" -y
Download Of File AutoPatcher .Net ModulesFailed. Skiping AfterDownload Action.
Download Of File Security Update For .NET Framework 2.0 SP2 x64 (KB2539631)Failed. Skiping AfterDownload Action.
*** ! FINISHED ! ***