Did you wait for a polling cycle on each agent manager that the machines connect to? If not, you can force a poll by right clicking on the agent manager(s) in question and select Scan Managed Computers Now.
Is it by any chance an HP/Compaq array? I use the Compaq MOM Paq and it woks great! That may be an answer for you. Just curious, I don't have a SAN yet; can you drop to a DOS prompt and simply do a DIR and get the size and usage like a physically attached drive?
It is possible that something did not enable properly. Would you be able to turn them both off, diskperf -N, reboot, turn them back on, diskperf -Y, and then reboot again? Just thinking out loud now, I wonder if it would help to turn the physical and logical on and off individually: diskperf...
Is it by any chance an NT or W2K server? Disk performance counters, both logical and physical, diskperf.exe -Y, are only enabled by default on systems beyond Windows 2000.
I had the same problem with an incompatible version of Java. Here is the link I use to upgrade any machine that does not seem to want to work:
http://java.sun.com/getjava/download.html
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