Your first port of call should be process monitor. Start capture, open an app, wait while the laggy issue occurs, then stop capture when the app appears.
Now you can comb through the app's history to see what it was doing.
To me this sounds like a timeout occured on one of the app's operations like check for internet connx or a file server connection. After the first use a cached response is used. Just a hunch anyway and not obvious why TP causes it.
Normally the answer is within the procmon capture.