Strange.
Now you mention Pro Tools. Is it still only using AAX plugins?
Are you having the issue, when you use the standalone applications?
Analog lab use the same settings the full applications does, because the factory presets apart from the multies is the same as in the full applications. So things that work in Analog Lab for not multies presets, should also work in the full applications.
Perhaps there is something gone wrong in your installs or files. Have you tried to clear the applications preferences, and if that did'nt work tried to reinstall the applications?
Keep in mind, that it in some synths can be preset programming related, if the sustain work. So in those cases it could help to know the name of the application and a preset, that give you issues. That can be tested.
But in example Piano V2 presets and other Piano preset should all work with the sustain pedal.