I assume that you mean, that it takes a long time to refresh the page. i.e. manager presses a button to upload new data, and it then takes a long time for the new screen to appear. If this is not correct, please ignore the rest of this post.
What are the loads on your server and network like?
Use the performance monitor on the server to check the CPU and network capacities.
Also check the event log, in particular look for events coming from w3svc, which is IIS. Errors, or warnings should give a clue as to the problem.
Check in IIS manager that you haven't limited the bandwidth or CPU time allotted to the timeclock program.
That said, it really needs be the supplier to advise you on this. They know how their software works and how it should be configured. Anyone else is just guessing. If they can't help, then perhaps you need to consider returning the software and cancelling your support contract - at least that's what you should tell their customer support dept.