The problem that workunits end in few minutes appeared again, so I set my BOINC manager not to get new tasks from WUProp@home.

At the time, my computer was crunching "The Riesel Problem (LLR)" task from PrimeGrid for about 2 hours and "Mini Collatz Conjecture" task from Collatz Conjecture for about 8 hours.

When the task from Collatz Conjecture was about to end, I had my BOINC manager get new tasks from WUProm@home.
At the beginning, my WUProp@home tasks ended in few seconds again, but as soon as crunching of the task from Collatz Conjecture ended, my WUProp@home program began to work fine.

18 Aug 2014 9:50:59 UTC -> got task from WUProp@home, which ended in about two seconds
18 Aug 2014, 9:51:08 UTC -> got new task from Collatz Conjecture
18 Aug 2014 9:51:16 UTC -> got well-working task from WUProp@home

I doubt that this problem is caused by anti-virus software and think that this may be problem (bug?) on WUProp@home data collector with PrimeGrid/Collatz Conjecture tasks (or genellaly long tasks?).

How do you think?

Have you disabled the Active and Passive Anti-Virus scans of ALL BOINC folders and subfolders (Program and Data)?

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I think I did it, but the problem appeared again.

running tasks:
PrimeGrid / The Riesel Problem (LLR) 6.24 (82.485%, running for about 41 hours)
World Community Grid / Mapping Cancer Markers 7.32 (87.901%, running for about 5.5 hours)

Exclusion settings of Microsoft Security Essentials:
files and places
files and places (2)
kinds of files
processes
(UI texts are in Japanese)

What should I do next?

Try these recommended changes to your settings in Microsoft Security Essentials/Windows Defender.
These are the settings I use and do not have any problems with any BOINC projects I run.

For Excluded files and locations:
You have >
C:\Program Files\BOINC
C:\Program Data\
C:\Program Data\projects\wuprop.boinc-af.org
C:\Program Data\slots\0
C:\Program Data\slots\1
C:\Program Data\slots\2
C:\Program Data\slots\3

You need to REMOVE ALL entries you have for ANYTHING WITH "BOINC" in it then ADD and SAVE the following two lines.
(I recommend using copy and paste to make it easier to add the changes. You need to add them one line at a time then click the SAVE button) >
C:\Program Files\BOINC\*.*
C:\Program Data\*.*
----

For Excluded processes:
You have >
C:\Program Files\BOINC\Boinc.exe
data_collect_v4_4.14_windows\_intelx86_nci.exe

You need to REMOVE >
data_collect_v4_4.14_windows\_intelx86_nci.exe

You need to ADD and SAVE the following lines >
C:\Program Files\BOINC\Boinccmd.exe
C:\Program Files\BOINC\Boincmgr.exe
C:\Program Files\BOINC\Boincscr.exe
C:\Program Files\BOINC\Boincscvctrl.exe
C:\Program Files\BOINC\Boinctray.exe
----

After making the changes noted above, Exit BOINC, wait about 1 minute, restart BOINC. Hope this works.

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Thank you for your answer.
My workunits seems to be running well now. (It recovers on getting a new task.)

I changed my settings like this:
Excluded files and locations
Excluded kinds of files
Excluded processes (1)
Excluded processes (2)

Should I exclude all folders in C:\ProgramData instead of C:\ProgramData\BOINC only?
(I'll try it if the problem occurs again.)

Thank you for your answer.
My workunits seems to be running well now. (It recovers on getting a new task.)

Should I exclude all folders in C:\ProgramData instead of C:\ProgramData\BOINC only?
(I'll try it if the problem occurs again.)

No you do not want to do that that could possibly lead to a virus/malware getting on your PC.

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I haven't changed the setting of MSE from Message 2329, and the problem continues to occur.
Sometimes workunits from WUprop@home end in short, and it recover to normal operation when my BOINC client finish crunching a workunit (not from WUprop@home).