DG,
JMP puts different things on the clipboard depending on what you select when you copy. If you
just select a graph with the fat plus tool, then you get an image on the clipboard. This image will be placed on the clipboard in several flavors, controlled by your setting in JMP > Preferences > Mac OS Settings. The panel there titled "Alternate Graphics Formats for Clipboard and Drag & Drop" show several available raster formats. The one vector format that is not listed but is always included is PDF. When you paste this into Keynote, you get an image like you want.
However, if you select a graph
and some part of the report, then this is no longer just a simple image. Now you are also placing multimedia text on the clipboard. This is placed in RTF format and JMP's internal journal format (a subset of JSL). When you paste this selection into Keynote, it prefers the RTF text and gives you a text box. The RTF includes the charts inline, but Keynote ignores those.
You can see the same behavior with Safari. Go to the JMP home page at http://www.jmp.com/ then right-click or control-click on the image in the lower right that says "Statistical Discovery. From SAS.". Choose "Copy Image" from the pop-up menu, then switch to Keynote and paste it into a slide. You get an image. But if you go back to Safari and choose "Select All" (command-A), copy-and-paste that into Keynote, you get a giant text box with no images.
JMP tries to be standard, but in the world of Copy and Paste, the recipient gets to choose what flavor of the data they want to take off the clipboard. We must put both RTF and an image there so that pasting works for Word too. It's unfortunate that Keynote prefers the RTF but doesn't display the inline images.
We made it a special case that if you just select an image in JMP and copy, you don't get RTF on the clipboard. That is there specifically for Keynote. But it means you need to copy-and-paste the image separate from the text. I'm sorry that it's confusing, but much of what you're experiencing is beyond our control.
Hope this helps!
--Michael