Two last entries are from two different apps, Automate simply haven't noticed change. Only way to make it aware of foreground app is back to launcher, then launch other app again. So lack of first block isn't issue here...
2014-09-26 15:44:11.384 INFO(645): App in foreground?
2014-09-26 15:44:13.431 USER(645): Foreground App 1m:com.llamalab.automate
2014-09-26 15:44:13.434 INFO(645): Screen off timeout set
2014-09-26 15:44:13.443 INFO(645): Display message
2014-09-26 15:44:13.456 USER(645): Timeout 1m
2014-09-26 15:44:13.457 INFO(645): App in foreground?
2014-09-26 15:44:17.291 USER(645): Foreground App 15s:com.google.android.googlequicksearchbox
2014-09-26 15:44:17.367 INFO(645): Screen off timeout set
2014-09-26 15:44:17.395 INFO(645): Display message
2014-09-26 15:44:17.398 USER(645): Timeout 15s
2014-09-26 15:44:17.400 INFO(645): App in foreground?
2014-09-26 15:44:20.691 USER(645): Foreground App 15s:com.google.android.googlequicksearchbox
2014-09-26 15:44:20.697 INFO(645): Screen off timeout set
2014-09-26 15:44:20.699 INFO(645): Display message
2014-09-26 15:44:20.708 USER(645): Timeout 15s
2014-09-26 15:44:20.723 INFO(645): App in foreground?
2014-09-26 15:44:22.987 USER(645): Foreground App 1m:com.llamalab.automate
2014-09-26 15:44:22.988 INFO(645): Screen off timeout set
2014-09-26 15:44:22.997 INFO(645): Display message
2014-09-26 15:44:23.007 USER(645): Timeout 1mcom.google.android.googlequicksearchbox is me launching chrome. For some reason automate detected the launcher instead. This happened once before when launching the clock app as well.
Ive noticed the same behavior actually. I tried to put as much information into the log as possible. This is a log using App Swap, but I'm going to try without using it and see if I get the same result.
2014-09-26 15:44:11.384 INFO(645): App in foreground?
2014-09-26 15:44:13.431 USER(645): Foreground App 1m:com.llamalab.automate
2014-09-26 15:44:13.434 INFO(645): Screen off timeout set
2014-09-26 15:44:13.443 INFO(645): Display message
2014-09-26 15:44:13.456 USER(645): Timeout 1m
2014-09-26 15:44:13.457 INFO(645): App in foreground?
2014-09-26 15:44:17.291 USER(645): Foreground App 15s:com.google.android.googlequicksearchbox
2014-09-26 15:44:17.367 INFO(645): Screen off timeout set
2014-09-26 15:44:17.395 INFO(645): Display message
2014-09-26 15:44:17.398 USER(645): Timeout 15s
2014-09-26 15:44:17.400 INFO(645): App in foreground?
2014-09-26 15:44:20.691 USER(645): Foreground App 15s:com.google.android.googlequicksearchbox
2014-09-26 15:44:20.697 INFO(645): Screen off timeout set
2014-09-26 15:44:20.699 INFO(645): Display message
2014-09-26 15:44:20.708 USER(645): Timeout 15s
2014-09-26 15:44:20.723 INFO(645): App in foreground?
2014-09-26 15:44:22.987 USER(645): Foreground App 1m:com.llamalab.automate
2014-09-26 15:44:22.988 INFO(645): Screen off timeout set
2014-09-26 15:44:22.997 INFO(645): Display message
2014-09-26 15:44:23.007 USER(645): Timeout 1mEnter code here...