As for 16-bit apps starting/running slowly, the following webpage will shine some light on what you can do to speed them up or have them run more efficiently/effectively.
http://is-it-true.org/nt/utips/utips35.shtml
(REMOVE any SPACES in the above URL)
In light of your other statement about other aspects of the system running slowly, I'd say there's definitely something else afoot.
For starters, try running disconnected from the network. That will let us determine if something associated with the network is the culprit. Often, delays can be traced to mapped resources no longer being available or other network-specific problems.
Hope this helps.
Ron