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It does indeed appear to be a problem in the interaction of Tangerine with OmniGraffle. I've done the following test:

1) create a document containing one shape from the "Magnetized" stencil.
2) fill it with colour.
3) colour its line.

If I pick a normal colour from the Apple colour picker (say, one of the crayons), I get a file of about 6300 bytes. If I do the same with a colour specified in Tangerine using CMYK, the resultant file has a size of about 1.5 MB. But if I use a colour from Tangerine specified using RGB, I also get a file of only 6300 bytes.

So clearly the interaction of OmniGraffle and Tangerine causes the inflated file sizes when the colour has been specified in Tangerine using CMYK.

I looked in more detail at one of the base64 blocks generated in the .graffle file: it had roughly 600KB of data in it (not including spaces). I know nothing of how CMYK is encoded, but that seems rather a lot for a uni-coloured box.

I can't tell if it's an OmniGraffle or a Tangerine issue: I've raised it with Tangerine Support.

Incidentally, Tangerine is a really neat little utility for handling predefined colour swatches (as long as you steer clear of CMYK, it appears).