Hey Joel,
A few things you can try to troubleshoot your issues:
- Check-out each layer separately to narrow down the problem.
- Make sure that you are not trying to check-out unsupported data types eg. Joins and Attributed Relationship Classes
And remember - ArcPad does NOT support custom marker symbols. Try using simple point symbols instead.
If you can't resolve your issues - please contact Esri Support (they have super-awesome ArcPad Support Analysts that will be able to help you!)
Hope this helps,
Hannah