There could be multiple reasons why this could happen. Here are a few:
User Permission: CA Client Automation uses the Local System Account to install software,
when you install the software locally it uses the Account you are logged into the system as.
Local Account do not have access to Remote Machine and User directories.
Fixed Location vs Variable Location: When you install software locally you select which drive and folder
you are running the software for, but when you install thru CA Client Automation, it uses the following folder:
...CA\DSM\ASM\TMP\activate<host_uuid>, so if you have fixed paths in you Scripts, it might fail.
32bit Software: We have customer copy files into windows\system folder or into the
64 bit section of the registry and then cannot find the data.
Since CA Client Automation is a 32 bit software, the data will actually get copied into
windows\system32 or the 32 bit section of the Registry.