I went away for a long trip shortly after I posted this, and forgot about it. Please excuse me!
The problem still exists, but I have much more detail around it. Apple have been looking into it, but have produced no solution. So here is the current story:
With Aperture 3.0.3, and OS 10.6.4 (but that doesn't matter - it's Ap3 that is the problem) I cannot get good prints using custom profiles for my Epson 1290 using Lyson inks. With Lightroom and Lightzone, I get good colours. If I choose the .pdf option from the Apple print window, and print from Preview (putting the correct profile into the Colorsync window) I get good colours with the 1290. And......from Aperture 3 using my Epson 230, which uses Epson inks, I get good colours.
Although profiles used to be in the Library/Colorsynch/profiles folder and that is where my custom profiles are, the profiles installed for the Epson printers are not. They are in a file in the root Library at Library/Printers/Epson/InkjetPrinter2/ICCProfiles, these are in an un-openable 'package', but I can look at them in the colorsync utility, and they are the same format as all icc profiles.When I use these installed profiles, the colours are not good, but then, the ink set is different from the Epson inks set, so that, by itself, doesn't mean much.
So it seems that Aperture can't use profiles for the Epson 1290; (it goes to this folder of packages for the Epson 230) although it uses them to make the .pdf image.
It seems weird to me. Any ideas out there?