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Ok, I found a refrence to this in the release notes for Patch 4 of ePO 4.
If anybody else has this issue then in the meantime the soloution is just to manually delete these temp directories.
I checked this with McAfee support that its ok to do this.
Our server had 800MB of temp files in there!!
Total length of time on call to Mcafee was 66 minutes and 17 seconds :)
Hopefully I have saved somebody else this hassle.