Within TeamCity if I trigger a build it all works correctly, however if the Scheduler triggers a build it does not seem to get all the files from VSS. I have clean checkout directory turned on, so I am not sure how it determines the patch for the VSS root.

Does anyone have any suggestions on how I can get it to always get all files, and create a new patch each time?
I have put the start of two build logs below, as you can see the first one has the correct 249mb, whereas the second only transfers 2MB. The files it doesn't get from VSS seem sporadic and not in relation to what has changed.

Manual Trigger

[23:57:49]: Checking for changes
[00:09:04]: Clean build enabled: removing old files from C:\Builds\Ab 2.0
[00:09:04]: Clearing temporary directory: C:\TeamCity\buildAgent\temp\buildTmp
[00:09:05]: Checkout directory: C:\Builds\Ab 2.0
[00:09:05]: Updating sources: server side checkout... (24m:53s)
[00:09:05]: [Updating sources: server side checkout...] Will perform clean checkout
[00:09:05]: [Updating sources: server side checkout...] Clean checkout reasons
[00:09:05]: [Clean checkout reasons] Checkout directory is empty or doesn't exist
[00:09:05]: [Clean checkout reasons] "Clean all files before build" turned on
[00:09:05]: [Updating sources: server side checkout...] Transferring cached clean patch for VCS root: Ab 2.0
[00:09:42]: [Updating sources: server side checkout...] Building incremental patch over the cached patch
[00:31:50]: [Updating sources: server side checkout...] Transferring repository sources: 124.0Mb so far...
[00:32:18]: [Updating sources: server side checkout...] Repository sources transferred: 249.46Mb total
[00:32:18]: [Updating sources: server side checkout...] Average transfer speed: 183.40Kb per second

Triggered by the Scheduler

[07:45:01]: Checking for changes
[07:55:09]: Clean build enabled: removing old files from C:\Builds\Ab 2.0
[07:55:22]: Clearing temporary directory: C:\TeamCity\buildAgent\temp\buildTmp
[07:55:22]: Checkout directory: C:\Builds\Ab 2.0
[07:55:22]: Updating sources: server side checkout... (24m:24s)
[07:55:22]: [Updating sources: server side checkout...] Will perform clean checkout
[07:55:22]: [Updating sources: server side checkout...] Clean checkout reasons
[07:55:22]: [Clean checkout reasons] Checkout directory is empty or doesn't exist
[07:55:22]: [Clean checkout reasons] "Clean all files before build" turned on
[07:55:22]: [Updating sources: server side checkout...] Building clean patch for VCS root: Ab 2.0
[08:19:46]: [Updating sources: server side checkout...] Transferring cached clean patch for VCS root: Ab 2.0
[08:19:47]: [Updating sources: server side checkout...] Repository sources transferred: 2.01Mb total