If you are using the 'Get Data For ArcPad' button to create your project, data et al. then you may need to do somthing in the wizard's 'Select Data' page. *see attacment
I'm making some assumptions here but hopefully it will apply to you to...
I'm choosing to 'Checkout for disconnected editing>Schema only' from my operational fgdb in the wizard and there's a checkbox from which I can choose an existing apl file. If you are using a similar workflow, every time you make edits to a script file or the apl file, you need to uncheck this box, which launches an 'Open...' dialog and repoint to your apl file again. This is because the selections you make in the wizard are saved in an *.apo file alongside your *mxd. This *.apo file contains not a pointer to your apl and script file but the actual binary encoding of those files in their entirety. Doing this essentially updates that binary in the *apo file.
I didn't find this documented anywhere.
Hope this helps,
Michael
[ATTACH=CONFIG]23520[/ATTACH]