If autovacuum is off on an 8.3 system, someone disabled it. Why was that done? It may be causing problems; especially as you say that running vacuum 'manually' fixes the problem for a particular process. What happens if you put it back on?

Also, isn't there an index missing from some query, or something similarly simple? Has ANALYZE been run regularly?

(Of course, this only applies when you are actually sure the db is the bottleneck.. )