Good to here that it sounds like you have tracked/narrowed the problem down.
About 10 years ago, we added an automatic defrag software to our servers and desk-tops PC's. This reduced the number of (odd) errors throughout the network.
Proper house-keeping on a system helps in the long run. Purging of Temp files and Caches along with regular Defragmentation of the discs keeps the machines running at a optimum level. This is one of the first things I do, if I get called to help out a friend with PC problems.
All desk-top PC's and servers on our network get full back-ups each night and our critical as well as get Defrag software installed before they are placed in service.
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