To enable the agent to run a Software Scan the Software Discovery task should be enable on all machines.
The agents then send the software inventory to the SS's or directly to the DM.
The Collect task on the System Engine then collects that data from the SS or DM and imports it into the database,
so you have access to it thru the GUI.
If the Engine is, there can be numerous reason why they are slow.
Can you create a 2nd engine and put the collect task there.
You might need an engine fix, which version are you on ?