I'm guessing that this is one of two known bugs, one of which is fixed, one that still needs to be addressed. We are planning a maintenance release soon, but in the mean time, there is a work around:
1. If you do the PASTE, but the logic does NOT show up, try again but this time...
2. Right after the "paste" command, if you get the "Paste Options" dialog where it asks you how to do "Inter-Code-Block Struct Field Handling" radio button group, select "NO, keep the original source...", then do the Search->Replace operation manually witinin the DESTINATION code-block of the ORIGINAL code-block structure with the DESTINATION code-block structure (e.g. replace "$Main" (clip source) with "MyCodeBlock" (clip destination))
3. If you do NOT get the "Paste Options" dialog, or you get it but it does NOT include the "Inter-Code-Block Struct Field Handling" radio button group option, let us know.