This is a spin off of Bug 74573. Copying and pasting with "skip empty cells" doesn't work correctly with regard to conditional formatting per discussion with Markus.
Confirming.
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Using attachment 93458 [details] I get the expected behavior after pasting with skip empty. WFM. Win 7 Pro 64-bit Version: 5.1.0.0.alpha1+ Build ID: b216cc1b8096eb60c27f67e8c27b7cd756c75e38 TinderBox: Win-x86@62-merge-TDF, Branch:MASTER, Time: 2015-11-12_00:06:20 Locale: fi-FI (fi_FI)