Onyx is performing normally - this behaviour is the same in v6 v6.5 & v7.
When you add a drop shadow etc you are effectively turning that part of the image into a bitmap. The rest of the image around this area remains a vector. It is not the case that Onyx cannot understand spot colors under shadows or grads - they are no longer there! your app has turned everything into a bitmap in that particular area - Onyx is working as it should and will display the basic CMYK values provided by the profile for that area. If you have “all icc profiles turned off” for the bitmaps, Onyx will display the raw CMYK values sent from the app (don’t forget to hit “apply” in Preflight in order to see any changes update)
Your app displays a single color space so it still looks fine in the app, but Onyx has a more advanced color engine. It can address CMYK bitmaps & vectors and RGB bitmaps & vectors individually within a single file. Thus it can apply one input profile to a CMYK vector in your file, and a different one to the CMYK bitmap in the same file for example. This accounts for the color difference you are seeing.
The area in your file you have turned into a bitmap by adding a drop shadow etc has one input profile applied, whilst the surrounding area which remains a vector has a different input profile assigned to it. It is designed like this to give you full control over your file. Many people like to turn off the profile for CMYK vectors to give the print more saturation & “punch” - for posters especially, whilst keeping the CMYK bitmap profile turned on to ensure any pictures within that poster have good color management applied for accurate skin tones etc
To resolve your issue you need to make sure BOTH bitmaps & vectors have the same input profile applied (or no profiles at all!) If you still see a difference after setting the profiles the same then you need to follow Jons advice and go to the rendering intents and set those the same as well.
You can use “color replacements” in Preflight as a work-around but it is more efficient to build a new Quick set with the input profiles & rendering intents set the same to save you from this manual process.
Also please ensure you have transparency switched on in the main RIP Queue screen. At the top go to “setup” - “Postscript” - “configure RIP” and in the dialogue box ensure that transparency is set to “on” and is ticked.
Sorry if this is long-winded but it’s difficult to explain otherwise.