Some comments to help gather diagnostics to identify root cause...

HCL Notes/Domino 8.5 Forum (includes Notes Traveler)

Subject:

In a quick review, none of the individual transactions take more than ~1/5 of a second.

It would be useful to know what was the 1st transaction number and last transaction for a specific operation. If you showed the console window, it would make it easier for you to provide this info. It can be shown by adding DEBUG_CONSOLE=1 into the Notes.INI.

Alternatively, if the delay is somewhere else, the following data collection during the 40 second operation could also help isolate the problem:

For the long delays, here is some information on how to collect data to help troubleshoot a specific delay:

Collecting data for a hang or long delay
If the Notes Client is unresponsive, and remains unresponsive, it may be hung.
If the Notes Client is unresponsive, and eventually becomes responsive, it is not hung, but may have had a long delay.

To determine the root cause of the hang or long delay, an NSD and Java core file need to be generated.
To do so, perform the following steps:
Open a DOS command prompt
Switch to the Notes data directory
Run ..\NSD (no args, assuming that the program dir is "above" the data directory
Run ..\NSD again for a long delay. Having 2 NSDs back to back will allow a comparison of the 2 states to ensure that it is in the same area of code at both points.
After the NSDs completes, supply these 2 sets of files, or do an ISA data collection
1. data\IBM_TECHNICAL_SUPPORT\nsd*.txt file
2. data\workspace\logs\java*.txt file "Java core"