Don't you have any problem on hardware (HDD) ?
Don't you use the server as file sharing (SMB on Windows)?
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Those numbers may or may not be representative because they just show a peak value, which may be just a one-off. Work with the stats.log produced by FMS instead. To have that you need to turn on 'usage statistics' on the logging tab.
In general, high 'wait time per call' indicates disk i/o problems. What is the speed of the drives and what else is the machine doing? Hopefully no Anti-virus scanning or indexing.
High 'elapsed time per call' usually is in indication of not enough processing power. Adding more processors / more cores / faster cores will help; but there could be a glass ceiling that can't be broken through until the design of the solution itself is made better to not need so much processing power.
The coffee cup may be completely unrelated to those numbers. Normally the coffee cup is an indication that FMS is suspending the user interaction and usually that is because FMS is doing a backup and needs a lock on the file, sounds like this lock takes much longer than it should. Check the backup schedules and make sure they are not set to perform a 'verification' at the same time. Turn that 'verify' off for the backups during working hours and turn it on for a nightly backup. If you have huge files and lots of backup schedules, then disk i/o clearly comes into play.