WHat is the one mail database? If it is mail.box that would not be a good thing. What I would look at is if the server is just having problems doing the other tasks because of the compact.
I guess there are a lot of things which haven’t been posted to inhibit suggestions.
One mail database is one user’s mail database (e.g. joeuser.nsf). When I compact one user mail database, mail.box gets full and doesn’t route to appropriate recipients. Once compact finishes, it routes fine…
Anything out of the ordinary wrong with the box. I just install a new server with windows 2000 and 6.0.2 CF2 and I don’t have this issue. I can route many mail messages while compact not just one database but many databases.
Without hard facts on the box and its configuration – it is hard to blanketly answer the question.