To all who posted in this forum, Matt and I have been working together on this and we have determined this is a bug:
NIM103949 - [Point features are not saved in ArcPad 10.2.1 when utilizing a workflow with a custom applet and closing ArcPad within 20 seconds.]
I brought the issue to the attentions of the dev team in Redlands and they believe the edits aren't saving right away due to individual processes that haven't been able to complete and store the edits until that time limit has passed. In Matt's case, we think it is due to the fact that multiple AXF files are being used in the applet and because each action made against a different AXF is a different process on the back end.
The workaround for now is to let your users know to leave the application open for more than 20 seconds so all the edits get saved.
Thanks,
Sarah