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The way OmniWeb handles favicons is inherited from WebKit, so the proliferation of icons is due to the way Apple has coded the Safari browser in the past, rather than anything that OmniGroup has done.

Have you physically deleted all the cache folders that exist for icons? It sounds like you haven't because the recent WebKit builds (including the one OmniWeb uses in the latter 5.7 sps) no longer create multiple copies of icon files and instead create a single database file. Perhaps that is the source of the issue you are experiencing? Also, if you have a folder called com.omnigroup.omniweb5 in your ~/Library/Application Support folder - delete it. No longer needed.