5000 files isn't very many to resolve, for a moderately powerful server.
Are your files binary of significant size? if your 5000 files are binaries, autoresolve will checksum them on your local hdd to compare against the checksum on the server (not the proxy, which is just relaying the information or files to you), and this can slow you down.
If you know beforehand that you are attempting a one-way resolve (eat yours on your hdd or eat theirs from the server), you can use the 'accept yours' or 'accept theirs' options to autoresolve and skip the checksum operation.
You can also contact your perforce db administrator and have them log the server actions. Maybe there are actions being run when you do your integration and resolve that are holding file locks, causing you to spin and wait until the locks are released. See the reference for 'p4 monitor show -a'.
For example, in our office, it's common on a Monday morning for everyone in the office to integrate up to their private branches and resolve.