There are no known performance problems with Netconfig on LMS 3.2. It sounds like command authorization could be the culprit. We have seen cases in the past where it takes quite a few seconds to verify the command is authorized on the AAA server. The more commands you have, the more this time adds up.
Would it be possible to temporarily disable this on one device for testing?
It might be worth investigating why this is happening. It could be due to network latency between the LMS and the AAA server. You could measure this using an IP SLA TCP connect operation from one affected IOS device to the AAA server (on tcp/49). While it won't measure the TACACS+ protocol itself, it will tell you how long the TCP handshake is taking. After that, you could look at AAA server statistics to see if the server is too bogged down. If you're using an external database, perhaps there is some latency there which can be fixed.