Comprssor 3.0.3 would be the problem if you have indeed updated with the combined Software Update 2008-02
You'd need to reinstall Compressor and update no further than 3.0.2 to fix the missing proxy issue.
It may be that you had some proxies generated prior to the update and since the update, no more proxies will auto generate during "full scans" of FCSvr. It would look like random proxies not being created but is more likely Compressor 3.0.3 has broken the proxies. All of us are suffering from this issue for weeks now.
http://www.apple.com/feedback/finalcutserver.html
