I have set up a custom user profile and workspace, and each time I close CAD I have to make both current it reverts back to defaults.
You've made changes to the default template and saved the template right? Are you opening the custom template when creating a new drawing?
How are you restarting ACA? If you do so from a desktop shortcut, you can include "switches" in the Target text that set the profile and workspace to be set current when that shortcut is used. /p is the switch used before specifying the profile; /w is the switch used before specifying the workspace.
Here is the Target line from a custom shortcut I set up for myself for ACA 2015:
"C:\Program Files\Autodesk\AutoCAD 2015\acad.exe" /ld "C:\Program Files\Autodesk\AutoCAD 2015\AecBase.dbx" /p "DWK ACA Imperial" /product "ACA" /language "en-US" /w "DWK Arch"