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answers:

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We configured TeamCity to do nightly builds based on a time trigger at 8pm on a standalone VCS root.

The root is configured to pull the tip. It is also set to do a clean checkout every time.

Has anyone else encountered an issue where not all modified files up to the point in time that the configuration is triggered on will be included. So for example we had a nightly build at 8pm on 8/13/2009, a checkin at 5pm, one at 6pm, but when the build triggered at 8pm on 8/14/2009 some of the changes are included and some are not.

I might be missing something really obvious here, but the result is a "successful" build that does not include all the changes!

Any help greatly appreciated.

A: 

I'd recommend you to submit an issue at the bug tracker. Enable debug logging and attach the VCS logs for the problematic checkout to the submitted issue. Refer to the Reporting Issues document for the details.

Otherwise, it's hard to say anything without the version information and the logs. Such issues can be solved much faster via JetBrains tracker/support than here.

CrazyCoder