If you are synching to Google Calendar in some cases alarms will not sync. Furthermore in all cases if you change or delete an alarm within Google Calendar's web interface that alarm change will not sync down to Pocket Informant.
In both cases the fault lies with Google Calendar. Pocket Informant relies on Google Calendar to provide changes and data to it to synchronize its data properly. In the first case Google sometimes does not provide the alarm data as part of the data feed to Pocket Informant. In the second case changing an alarm by itself for an event does not set the "updated" field which means that Pocket Informant has no way to know that the alarm changed and to update the data locally.
This bug in Google Calendar can be found described here at Google's bug tracking system: http://code.google.com/p/gdata-issues/issues/detail?id=153&q=reminder&colspec=API%20ID%20Type%20Status%20Priority%20Stars%20Summary