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We experienced the same issue too here. We contacted MS on this issue, and our issue was caused by Project Calculation Services (PCS) timing out against our our enterprise custom fields. MS sent us a new schedengine.exe which turn-off calcuation service against custom fields as a workaround to fix the issue.
At this time this issue should be fixed in the June 2014 server side CU according to MS. One other thing MS also asked us to try, but we didn’t do is to extend the timeout for the PCS from the default 30 seconds to something greater. Here are the steps that we got from MS –
1. Go to a farm box and start the “SharePoint 2013 Management Shell”.
2. Enter the following command:
Set-SPProjectPCSSettings – ServiceApplication “Project Service Application” –RequestTimeLimits 60000
Note: the “Project Service Application” name may be different on your server, but you can get this info from the Central Administration “Manage Service Applications” page.
The above command will increase the timeout to 60 seconds (double the default).
3. For each app-tier box in the farm, restart the “Microsoft Project Server Calculation Service 2013” service. This will cause it to reload and use the new settings.
4. Test applying updates to the given project.
Hope this helps. If you need a SQL script to identify all the failed task updates, please send me a email to firstname.lastname@example.org, and I will be glad to send it to you.
Joseph C. Yin MSBA (email@example.com)
Staff Systems Analyst