We have an Idealstor BA4U2E server and a 2000-TLYTE-2RSA (2-bay SATA rack enclosure) connected to it. We run Symantec Backup Exec 12.5 on it to copy between drives.
Lately our copy operation has been running significantly slower than it should. We also noticed, by remote desktopping into the server, that it has pauses for around 4-5 seconds, every 40 seconds or so. During these pauses everything in the system completely freezes. Monitoring the system with Process Explorer, we found that bengine.exe (the Backup Exec engine which does the copying) idles at 0 cpu for the 40 seconds, and then the whole system does it freeze, and then there's a huge I/O and CPU spike in the graph, during which bengine.exe was reading and writing to the disk. Monitoring even closer with Process Monitor does indeed find the 40-second gaps in which bengine.exe is doing nothing.
What is causing our copy operation to do this? How can we diagnose the problem?