Having a performance problem on a new BM3.8SP5 box and still trying to figure out why?

What I do notice is that, I must stop and restart BM to get performance back BUT when I do, I always see numbers like this on the Novell BorderManger Proxy Cache Server console window.
Cache successfully initialized with 143 objects (13929 files ignored).

Does this mean I am having some disk I/O problems and that cache files are not getting written to disk completely and they are getting corrupt? The proxy cache volumes were cleared this past weekend. I am always seeing a small number of objects that get successfully initialized.